LATECH, it should be a MAP sensor.
it serves as both MAP & BARO.
at key on the ECM stores the reading for BARO & then updates under WOT.
normally its mounted on the intake near the fuel pressure port.
probably moved inside for a cleaner install.
im not a fan of having it mounted low like that and with the port on the top side, over time fuel fumes can settle in it & condense.
the connectors in pic 2 & 3, the double wire connector i believe to be 1 of 2 for the AIR injection. the cut wires may be for the other AIR injection connector. or they could be for the EGR system, not completely uncommon for it to be tuned out of the chip also.
i don't believe its for coolant because he said it runs fine once warmed up.
i agree, its a HOTROD!, do something with those bolts.
64nailhead, the Megasquirt is impressive. you going with the MS2 or 3, or will MS1 be enough for you?