Before you go doing ANYTHING! Check what operating system is currently in your ECM. It is common practice to put an 02 OS in an 01 because the 01 OS is not mapped out the best, and is known to have many "ghost issues" when tuning. If your 01 was flashed to an 02, best case scenario flashing it back to stock 01 will corrupt your change engine oil counter making it always say to change your oil(this is documented in the efilive literature). More often than not it will brick your ecm(welcome to 01 lb7 life). And whatever you do, DO NOT flash it with a TECH 2 or anything using tis to go back to stock.
If it was mine, I would full flash in a 6006 02 OS with a V2, and use that for your base. For the TCM, flash it to the latest 01 OS completely stock. There are MANY MANY tables that EFILIVE put in there that should not be there. And messing with the trans tuning, even SMALL changes are a sure fire way to screw up your trans. Don't mess with the tire size or gear ratio settings, only changes to shift points, and I wouldn't touch any shift timing tables unless you're prepared to buy expensive hard parts when they get broken. And like most here are telling you, the bulk of your trans tuning is done in your ecm tuning.