You swapped engine and trans together? Sounds like it could be a balance issue. First crack each injector loose one at a time while the engine is running. Be careful of high pressure spray as it can inject into your hand and cause a very bad day. If you find one that doesn't make any difference...
A friend let me borrow his and another friend let me use his alignment rack to compare. It wasn't as accurate as his rack but pretty darn close. A lot of it is the user, it is much slower than the rack but especially for someone like me it would allow me to do it at home. Closest alignment...