It's a learning experience. 
I've learned over the years and hundreds of upgrades, wire management is a key element in an upgrade. Whenever I can, I secure all the wires that go to the shell up in the top out of the way and bring them to one common connector. That not only makes it easier to separate the shells or put them back together, it also keeps them from getting pinched when reassembling. A key is putting the wires where there is clearance, in something like the GP9, that precludes having them along the sides, it's better to have them at the top of the shell in the corners as a rule.
Oh, and NEVER use the crappy black electrical tape for anything! It turns to goo in a few months and is really difficult to clean up, not to mention it doesn't hold anyway! I use Kapton tape for a lot of taping chores, though I also use hot glue or CA adhesive to secure wires at times, it all depends on the situation.
