New Update, We replaced the fuel filters, OHM and Voltage checked all the sensors, checked the internal wiring , no issues at all found.
Flown almost 2 hours , then after one of the take off's when reducing power to MCP power for the climb, engine started the roughness, and rpm and MAP fluctuations.
After landing we tried again , this time only 1 time when MAP was 37 it started working rough , we reduced the power and again increased to full throttle , never had issue. Tried it for 10 times, didn't happen again even when reducing the power and made a test flight for 1 hour and no issues again.
Totally lost with this, no idea what is the problem , but i found out that my bowden cable is not safety wired to the servo motor , and also no loctite at the cable retrainer as mentioned in the AMM, wondering if that might be the case.. will do it tommorow.