Is it possible that you didn’t line up the camshaft and crankshaft sprockets at TDC before putting the chain back on? That would guarantee bad timing and rough running at best.

 

Thank you for your reply this is how I did the timing on the engine I put the motor at TDC camshaft at 12 crankshaft at 6 and then remove tensioner zip tied chain to the sprocket so it didn't move unbolted sprocket remove camshaft reinstalled new camshaft and bolted it back together would that keep the timing where it was or can it still be out of time doing it that way

 

I also assumed that the alignment pin on the back of the camshaft was the same as the one on the old one so I figured that it would put the camshaft back in the exact same position as the old one

 

I can’t be sure from that description, especially if the engine turned at all while the cam was out. Check out this video. It’s not the best, but there are some good sections at 2:40-3:30, 12:40-14:00, and 15:20-16:40. If your heads are still on, you have to be at TDC on the compression stroke so you can remove just one of the plugs on the #1 cyl and cover the hole with your hand to feel the air being pushed out as you approach TDC.

This also shows it.

http://www.engineprofessional.com/TB/TB011717-1.pdf

 

Another helpful idea is to swap the coil on the cyl with the current misfire code to a different cyl and see if the code follows it. If it does, the coil is bad. If not, swap the plugs from the misfire cyl to another cyl and see if the misfire follows the plugs. If not, do the same with the injectors.

 

 

did you find out you problem

 

I had a similar issue and found out that a couple of the pushrods popped out of place when tightening the rocker shaft bolts.