1999IOS

Both me and the wife drive Subaru's. She has a 2002 Legacy Outback (auto) and I have a 1999 Impreza Outback Sport (5 spd). I took the roof racks off my and was getting approx 28 mpg on the highway before I had engine issues. I am currently in the process of getting it back on the road but I am having a few issues. I had a timing belt issue and bent the valves on the original engine and figured it would be easier to just replace the engine, and do an oil pan and new clutch while I had the engine out. My car is a Federal emissions EJ22 (5 spd) and the engine I put in is California emissions EJ22 (auto). I used my cam and crank sprocket because the reluctor rings are different and replaced the timing belt and water pump. The car runs like its out of time but I have checked and rechecked the marks. I know there is a difference between auto and manual cam sprockets (2 pickups vs 7) but I am not sure if there is a difference between the Federal and California pickups. I tried my local dealer but they said there are multiple options but they couldn't help me without a VIN. If anyone has any ideas or info it would be greatly appreciated.