Biggest issue I have seen and this was fixing what a "PRO" screwed up was getting the injectors & coils in the right order at the PCM and then correcting the injector bank assignment and firing order in the tune. If you go by a Gen3 wiring diagram on the coils and injectors it will be wrong 100% of the time on a traditional small block. It all has to match or it will run terribly. It also had the left and right o2 sensors swapped and when the PCM tried to go into closed loop, one LT fuel trim went to 125% and the other 75%. Then getting good injector data is a MUST! Finally the trickiest part I have found tuning anything with the Blackbox and the 0411 has to be the way the PCM handles fuel enrichment for AE and the idle air stuff. I have found leaving the tune a little on the rich side helps the driveability tremendously with the bigger cammed setups.
Then again I have tuned far bigger challenges. A 232/240 @ .050 cam cut on a 110° LSA in a heavily modified TPI 383 running the 7730 speed density ECM. That one was fun just to get it leaned out enough so it would idle and you could drive it and tune it.
The LT1 I tuned was a 396 with 42 lb/hr junk bosch injectors and a GM 847 cam. Luckily I had injector data from my buddies 6.0L truck that has the same JUNK bosch injectors in it. The 0411 does not like Bosch injectors much and both still occasionally get codes for open injectors. Moral of the story there don't buy cheap Ebay garbage injectors if you want the thing to run well.
I like the Gen3 PCMs because you can do alot of cool stuff like add an Ethanol Flex Fuel sensor and run anything from straight gasoline to E85 and have the PCM adjust both the spark map and fuel delivery to secondary values you can set. I gained a good bit of power running E85 with no engine changes. The next engine in my Express van will be a 383 in the 11.5:1 range with aluminum heads and run E85 for power. Goal is 500 ft/lbs @ 3,500 from a small block. 383+ moded TPI is how you get there. Should still be able to get 400 hp out of it as well.
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