For the cyl 1 misfire code, swap the coil pack for that cyclinder pack with another one. If the code changes to another cylinder, you have a faulty coil pack. You can pick another one up from a junk yard dirt cheap. They are known to go bad, specially if there is any moisture present.

Fix the tranny mount
Connect all vaccum hoses properly
Track and fix the misfire
Change plugs, wires and oil/air filter

Run the car for a while before replacing O2 sensor. That code may disappear...

Good Luck