ALL ISSUES SOLVED! I decided to go hunting for the door limit switch. Found it and it appeared to click appropriately. I then decided to take out the door strap which I thought was broken and was intended to be a project for another day. I found a severed wire which, when resoldered to it's distal end fixed the limit switch error. Also, the screw that held the door strap to the door was missing (found in the bottom of the plastic) so I reinserted the door strap, connected it all back together and it worked too! It appears that the door strap retaining screw came out (WTF?) allowing the strap to swing around and sever the wires to the window limit switch. What a journey this weekend! Next weekend I'm going to try to put on the new top.
