OK now that I have them interfacing I am clueless as to how i should go about connecting it to the computer and handle sending data between the calc and the computer.

I have ti's link protocol information already I'm just lost as to how i should be doing this all of a sudden. any ideas?
The simplest (and most flexible) option here is to simply watch the link port lines and send a message on the radio link depending on what the exact state change was. Link starts with both lines high, and when you see (for example) the ring go low, you send a message to the other end of the radio link saying 'pull the ring low'. Similar signaling for the other state transitions.

Downside to that approach is you still need something that speaks the TI link protocol. If you have a serial link (black, grey, silver), that's easy. Otherwise, you have absolute freedom in the design, and need some new piece of software PC-side to interpret the data stream.

Bonus higher-throughput radio link: buffer protocol data by simply ACKing bits until a buffer fills or you hit a no-activity timeout, then send a single packet over the radio which represents multiple state transitions.
If I made it speak ti link protocol would say ticonnect/tilp be able to use it with out any real changes? (the device is registered as a com port on the computer but I have a feeling that means nothing)
No, not without a serial link (as I mentioned). Taking that approach, your base station just plugs into the serial link (eg silverlink or similar). Anything else requires a new backend for TiLP, or completely new software.

The blacklink depends on bit-banging signals (which doesn't work AFAIK with a usb-serial bridge), and I don't even know what greylink does, but it's probably not very compatible with things that just pretend to be UARTs either.
Well then I will probably do new software. I dont got me a silver link oh well.

@Kerm where can I get the documentation on what the gcn hub expects? So I can make sure it forwards data there right as well.
I believe that Merthsoft wrote some fairly complete documentation when he was putting his computer-side Chat program together. I think that I also have a lot of detail in the gCn Whitepaper:

http://www.cemetech.net/projects/item.php?id=35
  
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