The way i have done all of mine is keep the stock little red positive battery connector box that bolted to drivers side head area but just cut the wire where it passes through the connector then just add a new ring terminal to 1 new battery cable and run the cable to the battery where ever you want which was stock under floor on my truck. I like it out of the way. As for the harness the ecu can easily mount on drivers side firewall like mine. Remember they are made to sit down behind and below drivers side headlight. I have done a lot of swaps and my first harness I modified in like 2012 is still in my car running today. I weeded out everything and carefully wrapped it all back up…..total waste of time and effort. Now i just leave everything and just de pin the connector at the ecu and leave all the wires taped up in the harness and never even mess with or disturb anything downstream. The only place i need to cut or splice is in the mini fuse/relay box to make my connections all from the oem “C2” connector.