98 Dodge Dakota sport headgasket

A friend of mine recently had a water pump go out on his Dakota(2.5l magnum) ~100,000 miles) after his dad drove it about 15 miles the head gaskets were blown, it failed pressure tests, so his brother started to replace the gaskets when I went to help he had one already done so I finished the rest but I never really checked the other one now the engine is running but kinda rough so im wondering if it could be that he did something wrong(which I doubt) or if there may be a cracked head
from his dad driving it on bad gaskets also his check engine light was been on since the repair and that runs rough when warm