LaoR

Hello.
I am new to this forum and I am not really an electrician, but I have no other option left except to ask here, maybe someone had dealt with such problem before.
I have Evo X 2008 with TC-SST rebuilt, DEFI indicators installed and custom ECU modification. The problem, probably, is lasting for a long time, cause when I bought the car I did not notice that issue (yes, my mistake) but for last year I own it - it was always here.
The issue is when I stop the engine - the check mark appears on the dash for a second and again disappears:

Error that appears
After that, the scan using MUT3 shows that there is a timeout while communicating with AFS, SAS, Shift Lever, ECU and AWC or loss of data.
If we clean errors and start engine - everything works properly, errors appear only after engine stop.
We had checked a lot:

• completely removed security system with auto-start and turbo-time functions
• disconnected all DEFI gauges and control unit
• flashed the car's ECU back to stock software
• changed timing chain
• replaced ETACS (fuse box inside the car) twice - the first time it helped for 2 weeks, the second try has no success at all.

Sorry, that I cannot provide more details right now.
So, I am out of thoughts what can cause that problem. If someone can point me out to the cause I will appreciate.