Woof. Putting someone else's hacked harness back together. That is really a no fun position to be in.
So those cut wires up in the engine compartment I believe go to a couple automatic transmission specific devices. I believe the B/R and the B are supposed to go to the "downshift solenoid", and I believe the others (W/B and G) are supposed to go to the "inhibitor switch". Neither of those devices exist on the manual trans cars.
As for how to get that blue connector out of the white plastic housing.... Boy, are those things a biatch. I've taken a couple of those out, and it's a real PITA. There are little plastic tabs on the white housing that clip the connector shells into place. Four (at least) on each connector shell. You can see them on the empty holes. Thin tools inserted from the front to push the tabs out of the way enough to force the connector shell backwards out of the white plastic holder. PITA.
If you've got access to a parts car, I would say to just take a hacksaw to the old one to get all the connectors out, and then use a drill to eviscerate the connector shells on the other one to salvage the housing at the expense of the connectors. PITA.
I somehow managed to get a couple of mine out, and once they were out, I filed all the tabs down some so I could get them out again easier in the future if necessary. I'm hoping it's never necessary. I rebuild my engine bay harness, and in theory, I should never have to do that again.