Best to start with stock tune?

So I just finished installing the new setup into my 98 TA. The tune has been touched so many times over the years I'm wondering if it is better to start with a stock tune file. I've had the car since 04.

Was a bone stock automatic 98 TA. Had a little tune for shift points and a couple minor things.

Installed a 6-spd, tuned out the automatic stuff along with headers and all

Installed a 6.0L, had a lot of bugs that needed to be worked out so the tune was really messed with. By the time I pulled out the 6.0L, the tune was marginally ok. Very marginally.

Now the car has a 402 LS2 stroker and the tune is way off. Won't even idle without stalling, even when warm. I don't even know where to start with it, I don't know what has changed, anything.

Engine has a FAST 92mm intake and Nick Williams throttle body, Kooks longtubes, 231/244 .630"/.615" 112.5+2.5 cam. It is an LS2 block with a forged Lunati rotating assembly. Heads are Wilkes Performance CNC ported with 2.05/1.80 valves.

I'm kinda lost. I'm not great at tuning and am pretty new to it, but I want to start driving my car now that it is done.