So I was attacking the project of replacing the 3 motor mounts on the passenger side yesterday and everything was going great until I had everything basically back together, and I went to put the bolt into main mount and it doesn't seem to line up properly. I can get the holes to line up but when I go to put the bolt in it feels like it's cross threading any ideas as to why

 

Its possible that the threads got messed up, that bolt holds pretty much all the weight of the motor. I had to get a new mounting bracket(timing cover) since mine stripped out before I even got the bolt to proper torque spec. Or did you bolt up the two torque struts before trying to put that bolt it? They could have caused it to twist a little.

 

I did have the bottom strut hooked up but took it off thinking that was the problem so it is currently disconnected