One thing to remember is there are a TON of modifiers and limiters in the factory tuning. You have limiters based on coolant temp, trans temp, barometric pressure, torque limiters based on throttle position, limiters based on gear seleted, etc....there are as many limiters as there are tuning parameters.
If you've never ACTUALLY tuned a motor before, here is an example of what you're looking at. This is just the AFR table (in lambda) for the '88 based on RPM. If you look over to the left of the picture, you see a bunch of the tables / parameters / limiters (they go down out of frame) that you have to mess with to make it do what you want. If you miss a SINGLE limiter, you can be chasing your tail trying to figure out why it's not doing what you're telling it.....but this is where data logging comes in. Data logging and knowing HOW to read the data logs is where the real money is made. You can build what you think is the most whoop a$$ tune on the planet, but until you log it and see it's actually doing what you're telling it to do, you're just hoping that it is. This is why I don't go by "seat of the pants" testing. The seat lies when the wallet gets light....the dyno, track and data logs don't have those feelings attached.
If you don't know what lambda is, it's simply your AFR's represented on a scale of 1.0 vs 14.7 : 1. Example....an AFR of 14.7:1 would be 1.0, an AFR of 12.5 would be .85. In the picture below you can see I'm shooting for a target AFR of 11.6 while the car is on boost. This is for 93 octane pump gas, on race gas I'll go leaner up toward 12 - 12.5. If the car was running lean, let's say 17:1, you see something like 1.16.