Hard to say. The exhaust gasses leaks out , true, which doesn’t seem like it would cause much of a problem; but air also leaks in. The pressure at that point is positive some of the piston phases, and negative others, so an exhaust manifold leak will draw some fresh air into the exhaust stream. That fresh air will hit the O2 sensor and make the computer think the engine is running lean, and so the computer will inject more gas than is necessary for the proper mixture. An improper mixture can cause misfires.
Suggest to measure the fuel trims. If the trims are outside the normal range, best to fix all the exhaust leaks before assuming the problem is elsewhere. Otherwise, assuming the compression is good and there’s no other engine diagnostic codes showing, it sounds like you’ve pretty much done all you can do absent and injector cleaning treatment or replacing the injectors.