You don't need the knock sensors. I have been running without my rear sensor for several years. Crimp connectors are most likely not your problem. you said it runs good until it warms up, did you check the resistance of the coolant temp sensor?
Are you 100% sure all of the pins on the ECU connectors are good to go? Maybe you missed one?
Did you do ANYTHING else, even change the oil, while you were doing this wire cleanup? Don't stay too close minded that it is because you shortened some wires. Maybe you were changing the oil and knocked a sensor loose? I know I have had a couple situations when doing various work on my car that a wire pulled out from the sensor from age. Make sure all the wires are pinned into it's connector properly. Maybe you adjusted the idle control valve or throttle stop and didn't adjust the TPS properly? I'm not asking you to confirm any of these, just think about ANYTHING you did to the engine besides shorten and remove wires.
I would highly suggest going over the harness and verifying vs the OEM wire diagram with a voltmeter. The fact that your friend completely changed the power source for ignition and fuel tells me that he made some really poor decisions when rewiring. Is every single ground wire that was on the harness before, still there? Have you verified all of the grounds are going to where they should on the chassis/engine?
What is the gap on your plugs?