Why must I granny shift

I've had this issue since I got the car, 1988 245 +t LH2.2 EZK, where if I try to shift quickly and slam the throttle it hesitates for maybe half a second where nothing happens and then it goes like normal. I've done a lot of work to this car and nothing has had an effect on this problem. It only happens after I change gear.

I could shift my old stock 240 as hard as I wanted to and it would take it. M46 from that car is now in this one, but it was the same with the old M47. I'd like to fix it if I can, but I have no clue what could cause this..

What year was your earlier 240? If it was 86 or older it had a flat flywheel that weighs about 8lb less than the flywheel in an 88 manual car.

If you can't find any problems with what helps the engine accelerate. Stuff like the fuel pressure regulator, and ignition system. Then I'd look for some sneaky boost leaks.

The knock sensor triggering can make the engine hesitate. are you using premium gas?

I used the original M47 dog dish flywheel because I have a good clutch in it. 93 octane, my knocksense light doesn't come on when this happens. I upgraded my FPR and injectors awhile ago, which didn't change this issue.

Check for a small boost leak, and try cleaning the AMM.

I just wanted to be sure you weren't comparing the difference in the flywheels. If you go from one car to another it's a big difference.

Recently we put a chipped fuel ecu in 89740turbos car. It really seemed to smooth things out and help it run much better.

Another thought is advancing the cam a few degrees? Unless it is a T cam. That helps with low rpm running and maybe will pick up the next gear a bit better?

What turbo are you using? If this a Garrett T3 then that may be normal as the boost comes back up. They are less responsive than the mitsu turbos.

I'd want to see what the AFR's do when this happens, or better yet a datalog.
If it's boost related that would show on a gauge, I expect.

Kind of banging around in the dark without some clues.

Is this an OEM turbo ECU or a converted car?

It's in open loop when this happens so fuel pressure and injector size come into play, if you have altered the fuel pressure or the injector size that may be tipping it over one way or the other.
In open loop the ECU falls back to fixed programming and probably ignores any "learned" values used in closed loop.
How does it act in warm up? This is also open loop and may provide a clue. If it's rich in warmup it will probably be stupid rich in open loop hot.

Is there soot on your rear bumper?

Do you have a boost dump valve and a AFM? If so the BDV needs to dump into the turbo intake after the AFM.
If not the AFM signals a larger airflow than real and the motor goes dead rich. When the BDV closes things get more normal.