after installing the new headers on my car I am having an issue with the bolts not going in all the way in both from the cat end and the block end and I am afraid of snapping them from using too much force. The thing is they came out very easily without even having to use penetrating fluid but now they are giving me troubles going in, why is that happening and how can I fix this?
You say it is nuts going down on studs? Probably because the flange on the new headers is thinner than the flange on the originals. So the nut is having to run down farther down the stud. Essentially entering a zone where "no nut has gone before" which is thick with gunk or rust.
Run a thread-chaser or tap down each of the studs, should clean that up.