OK, more good touble shooting on the spark question, so it would seem from all your swap out testing, that the coilpack, plug, or plug wires aren't likely in question & with the fuel injector swap out testing, the #1 fuel injector isn't likely the problem either.
SO, that sorta leaves you looking at the compression question!!!!!
Maybe Murpheys Law is messing with you on the before & after miss!!!!
I was thinking maybe if the valves & seats were reworked on the back head, perhaps a piece of trash got somewhere it shouldn't, or maybe the head gasket got bumped when setting that rear head down in place, or maybe you missed torquing a head bolt back there, ect????
Anyway the compression test will tattle, if any of that has happened & is causing a problem.
The lower intake manafold gasket won't affect cyl compression.
BTW, do you have a CEL lit???? If so, pull & post the code Number/s, as they could offer up good clues.