The biggest issue is you might have made other issue while fixing the first and now you fixed the first and make a second, then you take it apart and fix the second but induced the first.
I can't believe its the handle after 15 yrs BUT in all this apart and together you have been doing maybe you did bend it a hair.
My thing would be start without the bolt, does it all go together without undue pressure, does the pins go in like they did before?
If it does then, take apart and install just the bolt and install trigger housing without the charge handle. Does it go together easy like before?
Does the bolt slide back and forth without much pressure?
Remember your hammer needs to be cocked and while pushing the bolt back you may have to overcome a slight hardness caused by the hammer touching the bottom of the bolt. If it is really hard, maybe your hammer isn't properly cocked OR jammed up on the sear causing the bolt to push the bolt up against the top of receiver to a stoppage. It must be low enough for the bolt to slide over it like it should properly.
So if all this is working at this point, take you bolt in hand and install your charge handle in the bolt groove and hold it down tight in groove. While doing this looks at the side of bolt and check to make sure the charge handle is fitting properly in the bolt and not sticking above the bolt body. If it is your firing pin may be causing it from properly fitting there.
If it is fitted properly, now install the charge handle and bolt in the receiver, holding the bolt in the receiver can you cycle this without the trigger housing?
Check to make sure your guide rod is sitting properly in the indented step.
If all this works now install the trigger housing, does the pin install as easy as before? If not then the bolt and trigger housing/hammer are rubbing somewhere wrong.
If the pins go in as normal before, then cycle the bolt and it should work. If not, remove that hammer and try this again without the hammer.
If it now works your hammer and bottom of bolt are jamming. So why isn't the hammer lower or allowing the bolt to slide over it?
If you do these steps you will find the issue if you are careful and not causing issues to move from one part not installed properly and then another the next time. Go slow and be patient. It really is not that hard especially if you go slow and check your parts on each step.
Post up what you find or where you get the issue again.