Moving my troubles out of introductions and here.
I've started working towards learning how this works, to try and get this car running right. It's never been 100%, but seems to have degraded over the last 3 years - granted a lot has changed on the car, and nothing to has changed on the efi.

It's a 730 ecm with a custom burned eeprom - that I don't know if it was burned to the car or an eBay purchase. I have however loaded the stock 730 bins from this site (90 y, 90 f 5.0, 90 f 5.7, s_aujp v6.0 and a manual transmission 5.7 conversion Dave w sent). The 5.7 conversion Dave sent ran the best of the burned chips, but was not as good as the custom burn i already had.
Running through various data logs, and trying to understand what all that means I've come up with more questions.
Hardware:
355 10:1 engine, forged and balanced crank, flat tops, gm lt4 hot cam with distributor gear, gm lt4 aluminum heads, roller valve train.
Car has brand new (<1000 miles) urethane mounts, timing set, balancer, exhaust gaskets and studs, plugs, wires, icm, coil, wires to coil and ecm, pickup coil, cap and rotor. Newish (<5000 miles) head gasket, map, o2, temperature sensors, transmission (t56 conversion) clutch, cross member and torque arm.
Base timing is set at 10 degrees which is as low as I can set it before the car dies with the est unplugged

Issues:
Continuous random misfire
Random Misfire under acceleration
Lack of power
Excessively rich exhaust (faint black smoke most times but nearly always burns your eyes)
Idling will slowly decrease until it can't run
Timing won't stay steady at steady rpm - I've always attributed this to timing light, but worth mentioning here
Random bucking and power drops at cruise on interstate
Usually after 8 minutes if driving it throws an ses light, but clears itself after another 10-12 minutes or a couple of shifts

Knock sensor: somebody here mentioned that exhaust banging around could set the knock sensor off.
How does the ecu react to an unplugged knock sensor?
Does it put it in limp mode, or just disable the input and throw a ses?
Does the knock sensor have any effect on fuel curve?