Adum Dum

This is not a post asking whether or not this swap is worth it, it's too late for me. I've already grabbed the engine from an 04 LL Bean and put it in the car, using it's original manual 5 SPD. I'm obviously running into the number of common issues with this swap, and would appreciate some help. Don't feel the need to answer every question, every bit helps. I can work through most of the pinouts slowly, but want to know if some things are entirely futile in my effort to get rid of CELs. It'll start with a bypass and run alright without the TCU in, but sometimes misfire with the TCU connected. I'm guessing this is because the transmission speed sensor is disconnected, which is something I can find the pinout for myself, as I already know which two connectors go together. I'm also receiving fuel line errors, likely in relation to the return lines. Is there anything else I need to purchase for this, or can I combine original modules to wire this in? My plan for the tachometer readout keeping my original gauges is to reduce the voltage with a resistor to drop it down to correct values. The place I really screwed up was in assuming AC units would be the same. I have the manual AC and heat controls and assemblies, but the harness is looking for an automatic. The pinouts to most connectors aren't anywhere near similar, so do I need to somehow find an automatic AC unit and controls for cheap, splice the Baja's climate harness in, or is there any amount of practical connector swap I can do to get there? If any of you have any knowledge on any of these questions, it'd be much appreciated.