They need to be straight up with the crank at zero. If they were off to the right and the crank was at zero after two revs it's wrong. One problem I've seen is how the timing cover is sloppy in it's mounting holes. That can lead to the marks being shifted a little. The cover must be level to the head and pushed straight down before tightening it. Do that and it'll be easier to get the cam sprocket marks lined up correctly. Ignition timing (CPS) also must be right.
You may have other problems too. Usually after I do that much work on an engine I go through a whole bunch of things before proclaiming it fit. Everything from leak checks to emissions to monitoring O2 and Vf. You shouldn't just jump in and drive it.
I also clean, inspect, and test many parts while off the car. Wastegate, sensors, alternator bearings and brushes, fan clutch, power steering pump, AC compressor, etc. Everything gets tested, calibrated, or serviced if it can be. Just pulling the engine apart and putting it back together isn't enough. If you want reliability the devil is in the details.