As I have been doing some research on stuff, I found what seems like a simple but vital key into what I may need to build an APRS Digipeater or APRS tracker. It is the Direwolf software. Seems it acts as a software audio based TNC and more.
It has all the feature I need to set it up as either Tracker or Digipeater build in. It even has routing. You could hook up 3 radios, if you had 3 audio interfaces on a computer and then have it setup to repeater packets from one interface over to other interfaces. It can even act as an IGATE. For a tracker, you can hook up a USB GPS puck and will read the NMEA data and then beacon out.
I am going to be testing it out today since I think I have everything I need. I have my laptop that I will install Direwolf on and configure, a BTECH APRS cable, 2 HTs (one for the Digipeater and one tracker), a Mobilinkd, and my phone (Which will run APRSDroid).
I post my results after I run my test.