I wouldn't really worry too much about portingout the heads too much.
If you remove all the carbon from them, polish the exhaust ports, deck or mill them 30 over to raise the compression, get stonger springs, the heads should be good
You should straight up have someone else just rebuild the bottom end because that'* no joke.
Get a cam (gt 1 *cough**cough*), comp cams lifters, along with the essentials, gaskets etc.
Then you can really benifit from bolt-ons such as, ported exhaust manifoldsor headers, bigger throttlebody(L67 one will work), blah blah
Ive got the same freaky combo of L36/4T60-E/ODB1*2 hybrid.
Or of you have lots of money you can get the 4.1l stroker kit...
The tranny should be fine unless you like one wheel burnouts and going WOT 24/7.
But if your trying to get a limited slip i know a couple places that offer one and i know were to get gear conversions as high as 3.73
To sum it up, it'* all about the dollars.