So I finally decided to get the TRD "Quickshifter" and use my $50 gift card. I called up the local dealer and they just so happened to have one in stock. Knowing about the shift boot issue I consulted my pops and he came up with a pretty ingenious solution to still utilize the stock shift boot collar to give a nice stock look with the new short shifter. Here are a couple pics:

http://zx2nr.net/images/scion/shifter/shifter_1.jpg

http://zx2nr.net/images/scion/shifter/shifter_5.jpg

http://zx2nr.net/images/scion/shifter/shifter_6.jpg