Could be anything from bad gas to fuel pump. But if it’s a recent new engine a lot of it could be valve timing causing it to bog out, the camshaft probably isn’t able to control the intake and exhaust valves at the right time causing your engine to shut down or bog out. I would just start with timing belt and adjust it to see if that helps the issue. It all sounds like just the new engine not being able to communicate and function properly. Hope that helps

Yea first check would be scan tool, then timing marks check.

If a bolt came lose and fell into the belt or the tensioner failed your could have skipped a tooth or two.

Hard to diagnose without actually checking marks.

it’s hard to tell what the cause of it would be. I guessed the timing since it’s a new engine or could just be the main computer not being able to adjust to the engine