DE Mazda2 light load misfire

Having a issue with my 2010 DE manual with very low km's which feels like a slight misfire at light load. Cold start and idle is great but as soon as you are at cruising speed there's a slight miss which almost feels like the brakes are being dabbed on and off very lightly. The problem also seems exaggerated with the a/c running. It still seems to have plenty of power up hills and feels a lot better once you give it some throttle.

I had to swap the engine in it as it was damaged so I'm lucky to have a heap of parts to throw at it. So far I've changed plugs, coils, throttle body, egr solenoid, cam sensor and the small valve on the inlet pipe just before the throttle body. Have also cleaned the maf and tried another battery. The car is not showing any fault codes on the scanner which is making it hard to narrow down.
Only thing I haven't done is relearn the idle by letting it sit for 20mins which seems to be a pretty common fix by the sounds of things (just found a youtube video on this). I have just put the original battery back in and have noticed the idle isn't so great now. Would this learning also affect light cruise?
I've only got the egr valve, iac and crank sensor left to swap out and hopefully eliminate.

I'm just about lost for ideas with this thing so any suggestions would be much appreciated.
 
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