Need help with RPM jump problem after 4EAT to 5MT swap

[Mech314]

I'm desperate, because I have tried everything and no solution found, so I'm humbly asking for a community's help and advice.

I am pretty sure that this is not my gear shifting technique but rather a car problem. I had other Subaru drivers tried my car and they all had the same problem, when I drove other turbocharged Subarus I never had anything similar, so this is just a problem of my car.. I guess.

Input:
2007 FXT Sport 4EAT with VDC canbus swapped with 5MT from 2003 WRX.
Flashed with MT rom.
Modified TCU to make ABS work.

Problem:
On acceleration when the engine is under moderate and high load when I shift gears I have a weird 500-1300 rpm spike. When I shift I push clutch and release the gas pedal completely. My tuner and friends suggested from the log that there is no fuel cut when I release the gas (or it is late). And that is it, we have no idea why this is happening, and what to do next.
I already tried:

Replaced throttle
Replaced gas pedal
Replaced BPV and BCV
Checked the car with disconnected MAF, MAP, O2, AVCSs.
Checked on MT and AT ROMs
Checked without TCU, ABS, VDC modules connected.

All the same, behavior doesn't change. Even in a limp mode under low boost, similar problem. I never had anything similar with 4EAT before swap, so most likely this is swap related, however I'm not sure at this point. I am sure that all the wiring done correctly with the car, because everything else is working perfectly good and the car runs very nicely with the exception of that problem.

Measured fuel pressure: 39psi with pressure regulator ON, 43 with pressure regulator OFF. 60ish psi under full throttle.

Here is the video of how it looks, this is obviously and extreme scenario, but it is very indicative of the problem.

RPM spike on gear shift - YouTube

RPM spike on gear shift - YouTube

I have logs but I don't know how to attach them here...
I'm asking for any ideas, this problem is super annoying, which makes me think about swapping the car back to 4EAT.

Addition:
Also my highway fuel consumption increased with 5MT from 23MPG to 19MPG, however it should be opposite in my opinion.

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