2001 Sonata 2.4L automatic tran rough shift

First the history up to this point…

I have been working on my friends 2001 Hyundai Sonata 2.4 DOHC, it started off with a transmission speed sensor, that replaced then the spark plug cables burned up, changed the cables and all four plugs, then it was fine for a week. His wife was driving the car and the car randomly shut off and wouldn’t turn over, got a code P0335 Crankshaft position sensor, got a new sensor, was a pain in the butt located inside the crank case behind the timing belt had to remove everything, installed the new sensor, realized the inner timing belt was shredded to bits so we replaced that, lined up all the timing marks, even opened up the valve cover and aligned the cams perfectly. Put it all back together and the car will crank but will not start. Its not locking up, it will turn over just fine, the valves are not bent either. But it keeps trying to turn over, the whole time we were working we had the battery disconnected and on a charger, while trying to turn the car on it cranks and sounds like it gets weaker and weaker with each rotation. I can smell gas, I check the spark plugs and ignition coils and I am getting spark…………….. The issues above have been fixed now ETCG suggested holding the gas while turning the car over, and it started perfectly..

Now onto the old but current issue, the vehicle shifts very rough, will sometimes jerk and stick between second and third gear. The jerking can be described as how it feels when you are at low revs and let off a clutch too much but the car doesnt stall. The check engine light will flicker on and off but will not stay on, and is not tripping a code.

Replaced transmission speed sensor

Replaced Crank shaft position sensor

Realigned timing after replacing inner timing belt

Car idles perfectly, starts perfectly but the shifting is still an issue.