Mazda 626 Idle issue and Coolant Cap

[Tractor Dan]

Trying to help my friend out. Her mazda 626 is either a 2000 or 2001, can't remember right off hand. I can check tomorrow for sure. Anyways her mom threw a belt and the genius drove it 40+ miles so slaughtered the stock engine. We got her a replacement from a yard and my mechanic put it in. He replaced all fluids, swapped over any parts from the old one that was needed, plugs, wires, and i think that's it. He may have done more my brain is just not working from a busy weekend. Anyways ever since she got it back it has had the issue where driving it is fine but at idle at a light it runs rough and doesn't really shake but vibrates i guess. Hard to describe. However when she puts it in neutral it idles smooth. So i'm a little stumped on this one. I just cleaned her MAF sensor tonight, we have replaced her air filter. I'm kindof wondering if it could be an ignition coil or possibly a faulty plug or plug wire? I know the plugs/wires are new but i have had plugs new out of the box be bad. Probably from rough handling at the store. So any ideas what it could be would be appreciated. She is on a tight income and so are her parents so i'm trying to help her out.

Also her coolant reservoir cap won't stay on because it has a chunk around the edge missing. Any ideas where i could get just the cap for this? The reservoir is fine. It's one of those caps that just pushes on the neck. Thing is any old cap won't work because it has the cap with nipples for the line between the cap and radiator and the overflow molded into it. So any ideas where i could get one would be appreciated. Gonna check a few more places and maybe have her call yards tomorrow.

It's a 2000 or 2001 Mazda 626. It has the 4 cylinder in it. Automatic. Standard emission engine not the California one. Engine that was put in had 80,000 miles on it.