1- The lower engine harness connects to the starter, alternator, and oil pressure/level senders. This won't prevent the engine from starting (assuming the starter engages and the motor turns over), nor should it trigger any DTC's.
2- DTC's will clear/reset without starting the engine, with the exception of some DM (Diagnostic Module) codes, which may require a re-start. The other modules only require cycling power on/off via the ignition switch; usually 10 seconds off after clearing codes will do it.
3- Digital code 096 (starter lockout) on the E-Gas module (which is analog code 6) should not prevent the engine from starting, if the starter is engaging. This code can cause an intermittent limp-home mode, but otherwise if the starter cranks, the engine should fire.
4- I have no idea what "OP" is but there is no "OP" module on the 124.034/.036 chassis. Sounds like the Palm scan is using an incorrect acronym for the Basic Module (BM, aka General Module) as the codes described are BM codes.
5- Please use
this document when translating 124.034/.036 error codes. DO NOT trust any translation from the Palm Scan.
6- Before going crazy pulling the fuel tank, check fuel pressure at the Schrader valve on the fuel rail, near the front of the intake manifold. When you turn the key on, the fuel pumps should run for 2 seconds, and pressure should be 40-50 psi (approx). If you are getting fuel pressure at the rail, it's not likely you have a problem with either the pumps or tank strainer.
7- You said you replaced the upper engine harness, was it a newer harness, dated 2000 or later?