The 99's had 19lber, the '05 had 24lb or 38lb'ers, depending if it was a flex fuel truck.
I doubt you have the flex fuel injectors, it would be fouled out by now and smoking black very badly, no power at all, but with lots of sputtering and smoke.
If you have the 24lb injectors in there and I tuned for 19lb'ers, then it'll still drive and drive just fine at wot, it may be a bit rich, but still run.

-What do the ltrims look like?
If the are 25+ or 25-, then something is up. Maybe bad 02's, what 02's did you use for the truck?
-I'd get the fuel pressure checked under a load
-You shouldn't have any trans codes popping up. Is the truck starting out in second?
-What about all those wires that were unidentified? Did you get those figured out?

Keep us updated, we'll get it,

allen