RPi3 box troubleshooting

Greetings, all! I decided to tinker with the RPi by making a piratebox. I am using:
RPi 3+ (the latest one w/ built-in wifi)
TP-LINK TL-WN822N v3
Power supply battery (not using this yet, just a wall outlet for now)

I have followed all steps on this tutorial: [piratebox.cc]
And this one: [piratebox.cc]
which I think is based on this discussion: [forum.piratebox.cc]
I have also read several other forum posts, including this one about disregarding the Pi3's built-in wifi: [forum.piratebox.cc]

I am having an issue activating the usb wifi instead of built-in. While carrying out the commands in the steps linked above, at one point I was actually able to connect to the piratebox and check out the chat, forum, etc. and everything seemed to be working. Even though I had changed:
/opt/piratebox/conf/piratebox.conf
/opt/piratebox/conf/hostapd.conf

to reflect wlan1 and phy1 instead of wlan0 and phy0, it was still not using the usb wifi. I know this because I unplugged the usb wifi adapter from the Pi and was still able to cruise around the piratebox web interface. Now that I've exhausted the options in the above links, I cannot even connect via built-in wifi. Right now I'm connected via ethernet through my router to my pc. I am running Ubuntu MATE 16.04, accessing the Pi via terminal.

Here are some file configurations based on all the tutorials I've followed so far:

[alarm@alarmpi ~]$ iwconfig
wlan0     unassociated  Nickname:"<WIFI@REALTEK>"
          Mode:Auto  Frequency=2.412 GHz  Access Point: Not-Associated
          Sensitivity:0/0
          Retry: off   RTS thr: off   Fragment thr: off
          Power Management: off
          Link Quality:0  Signal level:0  Noise level:0
          Rx invalid nwid:0  Rx invalid crypt:0  Rx invalid frag:0
          Tx excessive retries:0  Invalid misc:0   Missed beacon:0

lo        no wireless extensions.

eth0      no wireless extensions.

wlan1     IEEE 802.11bgn  ESSID: off/any
          Mode:Managed  Access Point: Not-Associated   Tx-Power=1496 dBm
          Retry short limit:7   RTS thr: off   Fragment thr: off
          Power Management: on

Contents of /opt/piratebox/conf/hostapd.conf

interface=wlan1
#driver=nl80211
driver=rtl871xdrv
#driver=rtl8192cu
ssid=PirateBox - Share Freely
hw_mode=g
channel=1
#auth_algs=1
#ieee80211n=1
ieee80211n=1

Contents of /opt/piratebox/conf/piratebox.conf

#########
## Config for pirate-box WWW Release
##  written by Matthias Strubel  (matthias.strubel@aod-rpg.de) 2011-02-22
##  licenced by gpl ; feel free to improve or send me feedback
##
##  2012-04-12 Created
##  2012-06-08 Changed IP Stuff to generating dnsmasq.conf stuff
##             ADDed SubConfig for IPV6 config
##             Changed Order of config
##  2013-08-14 Added timesave url
##
########

#######
## Configuration help
##    If you plan to use one laptop as the piratebox:
##        Set DO_IFCONFIG , USE_APN, USE_DNSMASQ to yes
##    If you plan to run a two component setup (one router and one providing the storage+$
##     connected with ethernet:
##        Set DO_IFCONFIG , USE_APN, USE_DNSMASQ  to no
##        Configure your ethernet eth0 (or whatever) to a static IP
##        force your router to publish the  HOST Option with your static IP; in case of d$
##        Have a look at [wiki.daviddarts.com] for futher instructions
##
##    You may deactivated severall option as needed. It's flexible.


#----------------- Folder Configuration  -------------------#

PIRATEBOX_FOLDER="/opt/piratebox"
WWW_FOLDER="/opt/piratebox/www"

#Do not change untill really needed.
PIRATEBOX_PYTHONPATH="$PIRATEBOX_FOLDER/python_lib"


#Datafolder  , where is you usb-stick // drive mounted
SHARE_FOLDER="$PIRATEBOX_FOLDER/share"

#Upload Folder
# Change this if you want to user uploaded data in a subfolder
#   Make sure the folder exists
# UPLOADFOLDER="$SHARE_FOLDER/Upload"
UPLOADFOLDER="$SHARE_FOLDER/Shared"

#----------------- Startup Configuration  -------------------#
# Which Steps has to be done

#Do network config
DO_IFCONFIG="yes"

#Do IW config - setting up a wlan0 interface with iw
#  for some wifi-cards required
DO_IW="yes"
#Iw physical interface
PHY_IF="phy1"

# Check if interface exists
#  should be set to yes if you use a USB wifi card
PROBE_INTERFACE="yes"
#  wait how many seconds until throw an error
PROBE_TIME=10

#Start services...
#   act like a apn  / <yes|no>
#    please have a look @ hostapd.conf ; you may need to change some options, regarding w$
USE_APN="yes"
#   act like dns&dhcp (dnsmasq)
USE_DNSMASQ="yes"

#HOSTNAME  ... if you really want to change it, plz change:
#    bin/droopy
#    conf/hosts
HOST="piratebox.lan"

#----------------- Configuration for DNSMASQ & IF-Setup  -------------------#
# Name of the wlan interface
INTERFACE="wlan1"
# On which interface DNSMASQ should listen. -i is the parameter for dnsmasq
# Make it empty to disable
DNSMASQ_INTERFACE="wlan1"

#Brdige add interfacce (setr yes to enable bridging)
DO_BRIDGE="no"
BRIDGE="br-lan"

#Network
NET=192.168.77

#IP-SHORT (is stringed together)
#  Which IP is your Box??  i.e. 1 => 192.168.77.1
IP_SHORT=1

#DHCP LEASE Start
START_LEASE=10
#DHCP LEASE End Range
END_LEASE=250
#Leasetime  (When should the client renew it's IP)
LEASE_DURATION=12h

# Where is the leasefile stored to?
LEASE_FILE_LOCATION=$PIRATEBOX_FOLDER/tmp/lease.file


# Define the netmask
NETMASK=255.255.255.0

#SET IP for ifconfig stuff - DON'T CHANGE
IP=$NET.$IP_SHORT

#Load Config about ipv6 stuff - DON'T CHANGE
 . $PIRATEBOX_FOLDER/conf/ipv6.conf

#----------------- Configuration for the pure piratebox -------------------#
## droopy, webserver, shoutbox- and forum-server

## Timesave file for non RTC devices
TIMESAVE="$PIRATEBOX_FOLDER/share/timesave_file"

#On non OpenWRT you can use the default output format
# as an input format. For OpenWrt you need to specify +%C%g%m%d%H%M
# The content is exchanged during makefile processing and image build
TIMESAVE_FORMAT="+%C%g%m%d %H%M"

#Start droopy? - Enable upload?
DROOPY_ENABLED="yes"
#Image-SRC
IMAGENAME="piratebox-logo-small.png"
IMAGE="$PIRATEBOX_FOLDER/src/$IMAGENAME"
DROOPY_TXT=""
DROOPY_PORT="8080"
# Set correct permissions for an uploaded file
DROOPY_CHMOD="755"
DROOPY_USERDIR=""
# Uncomment line below for adding directory feature
#DROOPY_USERDIR=" -u True "

#Use UserId from lighttpd for droopy  (use on ext-filesystems)
DROOPY_USE_USER="yes"

#Configuration for chat  (If you decide to move the chat folder, you have to change /opt/$
CHATFILE="$WWW_FOLDER/cgi-bin/data.pso"

#Generated File
GEN_CHATFILE="$WWW_FOLDER/chat_content.html"

#Generated File for DiskUsage
GEN_DISKFILE="$WWW_FOLDER/diskusage.html"

# Reset Shoutbox on Startup?
RESET_CHAT="yes"

#Inititiation Chat-Message
CHATMSG="<div class='message'><date>00:00:00</date> <name>PirateBox:</name> <data class='$

#Activate Global chat
# Still experimentall!
GLOBAL_CHAT="no"

#On which broadcast address should it send
#  Take care on the syntax!!
GLOBAL_DEST="[ #255.255.255.255# , #10.255.255.255# , #$NET.255# ]"

#------------------------ Additional configuration for lighttpd
LIGHTTPD_USER=nobody
LIGHTTPD_GROUP=nogroup


#------------------------ Hook in user-config
.  $PIRATEBOX_FOLDER/conf/hook_custom.conf

When following the guide here: [piratebox.cc]
I looked into the /prebuild/hostapd/ folder to see what was available:

[alarm@alarmpi ~]$ cd /prebuild/hostapd/
[alarm@alarmpi hostapd]$ ls
hostapd-2.5-1-armv7h.pkg.tar.xz
hostapd-8188eu-armv7h.pkg.tar.xz
hostapd-8192cu-armv7h.pkg.tar.xz
hostapd-RTL8188C_8192C_USB_linux-v4.0.2_9000.20130911-1-armv7h.pkg.tar.xz

I didn't know if I needed the 3rd or 4th file listed. I started with the 4th one, and when that did not work quite correctly, I chose the 3rd and ran this as part of step 1:

pacman -U /prebuild/hostapd/hostapd-8192cu-armv7h.pkg.tar.xz

When I check system status, I see:

[alarm@alarmpi hostapd]$ systemctl status piratebox
* piratebox.service - PirateBox Service
   Loaded: loaded (/etc/systemd/system/piratebox.service; disabled; vendor preset: disable
   Active: active (exited) since Mon 2016-02-22 14:40:17 UTC; 3 months 12 days ago
  Process: 243 ExecStart=/opt/piratebox/init.d/piratebox_alt start (code=exited, status=0/
 Main PID: 243 (code=exited, status=0/SUCCESS)
   CGroup: /system.slice/piratebox.service
           |-288 /usr/sbin/dnsmasq -x /var/run/piratebox_dnsmasq.pid -C /opt/piratebox/con
           |-293 python /opt/piratebox/bin/droopy -d /opt/piratebox/share/Shared -m  --chm
           `-311 /usr/sbin/lighttpd -f /opt/piratebox/conf/lighttpd/lighttpd.conf

Jun 04 23:25:00 alarmpi dnsmasq[288]: read /opt/piratebox/conf/hosts_mesh - 0 addresses
Jun 04 23:25:00 alarmpi dnsmasq[288]: read /opt/piratebox/conf/hosts_generated - 1 address
Jun 04 23:25:00 alarmpi piratebox_alt[243]: /opt/piratebox/bin/delete_empty.sh: line 12: cd: /opt/piratebox/share/Shared: No such file

Jun 04 23:25:00 alarmpi piratebox_alt[243]: 0
Jun 04 23:25:01 alarmpi piratebox_alt[243]: Generated HTML-Shoutbox File.
Jun 04 23:25:01 alarmpi piratebox_alt[243]: CRITICAL: /opt/piratebox/share/Shared modified 1206 minutes ago. Threshold set to 5 minutes
Jun 04 23:25:01 alarmpi piratebox_alt[243]: Generated HTML-DiskUsage File.
Jun 04 23:25:01 alarmpi piratebox_alt[243]: Starting lighttpd...
Jun 04 23:25:01 alarmpi piratebox_alt[243]: 0
Jun 04 23:25:05 alarmpi systemd[1]: Started PirateBox Service.
lines 1-20/20 (END)

I read where someone suggested running:

sudo /opt/piratebox/rpi/bin/wifi_detect.sh

So I did and I see this:

[alarm@alarmpi hostapd]$ sudo /opt/piratebox/rpi/bin/wifi_detect.sh
[sudo] password for alarm:
Found nl80211 device capable of AP mode...
warning: config file /etc/pacman.conf, line 98: directive 'IgnorePkg' in section 'aur' not recognized.
:: hostapd and hostapd-RTL8188C_8192C_USB_linux are in conflict. Remove hostapd-RTL8188C_8192C_USB_linux? [y/N] y
:: Proceed with installation? [Y/n] y
[alarm@alarmpi hostapd]$

I am not sure what I've done wrong. Can someone point me in the right direction?