So, I opened package content and looked for "pytivo" and opened it in terminal and got this:
-bash: /Users/Alex/.profile: No such file or directory
/Volumes/Drive\ Genius\ BootWell/Applications/pyTivo.app/Contents/MacOS/pyTivo ; exit;
Alexs-Mac-mini:~ Alex$ /Volumes/Drive\ Genius\ BootWell/Applications/pyTivo.app/Contents/MacOS/pyTivo ; exit;
INFO

yTivo:Last modified: Mon Aug 14 15:58:18 2017
INFO

yTivo

ython: 2.7.13
INFO

yTivo:System: Darwin-15.6.0-x86_64-i386-64bit
INFO

yTivo.beacon:Scanning for TiVos...
INFO

yTivo.beacon:Master Br - 192.168.86.111
INFO

yTivo.beacon:Basement - 192.168.86.114
INFO

yTivo.beacon:Family Room - 192.168.86.106
INFO

yTivo.beacon:Announcing shares...
INFO

yTivo.beacon:Registering: TiVo Recordings
INFO

yTivo

yTivo is ready.
INFO

yTivo:192.168.86.106 [09/Sep/2017 14:01:11] "GET /TiVoConnect?Command=QueryContainer&Container=%2F&DoGenres=1 HTTP/1.0" 200 -
INFO

yTivo:192.168.86.114 [09/Sep/2017 14:01:11] "GET /TiVoConnect?Command=QueryContainer&Container=%2F&DoGenres=1 HTTP/1.0" 200 -
INFO

yTivo:192.168.86.111 [09/Sep/2017 14:01:11] "GET /TiVoConnect?Command=QueryContainer&Container=%2F&DoGenres=1 HTTP/1.0" 200 -
INFO

yTivo:192.168.86.106 [09/Sep/2017 14:01:11] "GET /TiVoConnect?Command=QueryContainer&Container=TiVo%20Recordings&ItemCount=0&SerialNum=74600119024F64E HTTP/1.1" 200 -
INFO

yTivo:192.168.86.114 [09/Sep/2017 14:01:11] "GET /TiVoConnect?Command=QueryContainer&Container=TiVo%20Recordings&ItemCount=0&SerialNum=74600119043D2CF HTTP/1.1" 200 -
INFO

yTivo:192.168.86.114 [09/Sep/2017 14:01:12] "GET /TiVoConnect?Command=QueryContainer&Container=%2F&DoGenres=1 HTTP/1.0" 200 -
INFO

yTivo:192.168.86.111 [09/Sep/2017 14:01:12] "GET /TiVoConnect?Command=QueryContainer&Container=TiVo%20Recordings&ItemCount=0&SerialNum=74600119047CB8C HTTP/1.1" 200 -
INFO

yTivo:192.168.86.106 [09/Sep/2017 14:01:12] "GET /TiVoConnect?Command=QueryContainer&Container=%2F&DoGenres=1 HTTP/1.0" 200 -
INFO

yTivo:192.168.86.111 [09/Sep/2017 14:01:12] "GET /TiVoConnect?Command=QueryContainer&Container=%2F&DoGenres=1 HTTP/1.0" 200 -
So, something seems to be working.
And this is what I get with Pytivo tray:
Last login: Sat Sep 9 14:01:07 on ttys000
-bash: /Users/Alex/.profile: No such file or directory
Alexs-Mac-mini:~ Alex$ /Volumes/Drive\ Genius\ BootWell/Applications/pyTivo.app/Contents/MacOS/pyTivoTray ; exit;
So here is a thought. Since this other drive is also a recovery boot drive could Pytivo be installing onto that System folder instead the the primary one. I will try trashing all the files and beginning over into primary drive, then move the programs over to the drive I want them to run from. Maybe that is the key?