Megasquirt Sync loss and timing way off
 

Dear miata geeks,
I'm having some troubles with my car since I replaced the engine (previous one was drinking too much oil). The original one did not have any issue with the msq3
It's an european Mazda MX-5 sport with the 1.8 vvt engine. The issue is that the megasquirt looses the sync with the rpm above 4800rpm (here https://drive.google.com/file/d/13TDaMN7-l9G1Y84fq0Lkktmb25t-j0Mr/view?usp=drivesdk you can find a composite log of the trigger inputs) and it seems that the ECU does not see the 1-2-1-2 cam input anymore at those rpm. On top of that I cannot set or see the base timing because with the timing light in place I don't see the 2 notches on the main engine pulley, they are not aligning with the marks on the timing belt cover but they are below the orizontal axis of the pulley (like it's mirrored).
I tried changing both cam and crank position sensors, change the valve cover, check and recheck the timing (cil 1 at TDC, pulley mark shows TDC as well and the cams aligned with the signs on the head) checked the ground with a multimeter (basically no load) and it reads 0 ohms but nothing worked.
Also in attachment my timing situation.
Thank you in advance for your support
Have a nice dayhttps://cimg6.ibsrv.net/gimg/www.mia...a40e37471.jpeg
https://cimg7.ibsrv.net/gimg/www.mia...2c7ce115f.jpeg

The timing light problem sound like you're putting the clamp on the wrong plug wire if it's running but the timing shows 180 on the pulley. VVT coil packs have a lot of snaking wires so double check you've got your timing light on the right plug. You need to tell TunerStudio to set the car at something like 10 degrees and verify timing and change your ignition offset to match (stock NB2's is like 5.5) Did you gap your CPS?