Do you feel comfortable trouble shooting someone else's mess? With that amount of mods and having issues I would stay away personally, even at 16k. Find a car that is either mostly stock or completely sorted. You'll have a hard time even knowing what year or model parts you need if any aspect...
I think that the STI short shifter is the same size as 01 and older linkages.
edit
**based on this description**
http://www2.kartboy.com/x4/product.php?productid=16171&cat=253&page=1
Do you have the factory short shifter linkage? They sell a specific Kartboy lever for this and it's labeled as "narrow".
**edit** I don't think it's actually labeled, but rather marketed as the narrow version.
I only have a 27" top box but you should look into the stainless steel Kobalt boxes at Lowe's.
Don't bother with the painted Kobalt's or Craftsman, in my opinion the drawer guides all suck.
If you have time (doesn't sound like it!) there are deals to be had on bigger name brand boxes on...