If you had to do it over, which program would you go with?
I never ran the TST regular with a stock turbo, but did with a slightly bigger HTB2 62/12. When it didn't have all the codes and wonky fuel timing issues, it ran great. When stacked with a low end pressure box, like the VAC3. 1, it did even better on the low end even though as Tomeygun recently found it suffered on the high end due to the VA programming-for-the-towing crowd. After getting the run around from TST (like others on this board have with early '03 HO) I said screw it and sold it.
Then I went injectors w/ VA box, then DD TTPM, then Edge Juice. All served me extremely well, with awesome customer service after the sale, but I still secretly missed the multiple adjustability of the TST. Then AK Ram posted on DTR that the mother-of-all TST programs was becoming "officially" available again - the "03 Twins Program". It was the program that has the least amount of code and driveability issues. So I bought it 2 months ago and haven't been happier - no more codes like I had last time (knock on wood!).
In the meantime, I hooked up a rail pressure gauge and started seeing low pressure issues with injectors + any duration box. So a lot of research and PMs later, I ended up with a TS MP-8 (new Ramifier) with infinite adjustability. It has the awesome low end feel of the VA, but doesn't peter out on the high end unless the rail is drained. I figured that with bigger injectors + aggressive pressure box, I would have to worry less about high rail pressures anyway.
So what do I normally run on? 40-50% MP8 & 1x0 (timing only) on the TST. I do this mainly to keep the fuel atomized plus get the advanced injection timing benefits. The MP8 even by itself is awesome.
What's the most I've dared to run on? same 40-50% MP8, but 4x4 on the TST. This combo flat out scares me. It is so violently aggressive that I can't comprehend fast enough what is happening via the gauges except to hold on the wheel. What's even more scarier is that it looks like I might have a hair bit more rail pressure left. What's even, even more scarier is what if there was a high pressure pump capable to support the remaining 5x5 levels?
I can't wait to dyno this...
Anyhow, to answer your question, for a stock truck the regular TST with some mods will give you the most useable adjustability in terms of all the various permutations of 9x9. However, just do a search on here when the 03 TST first came out (the "Twins" program) and you'll find tons of posts about people popping stock turbos as well as even some aftermarket ones.