If I hear another post about ditching the knock sensor, I want to see proof of why you would do this. Enough about that. (not aimed at you)
Knock sensor is NOT easily fooled by engine noise, it responds to a specific frequency. You can't tell me that something that can tell the difference between a 305 and 350 simply by "noise" is something that will easily be tricked by other noises.
Yes, they CAN react to things other than what they are designed for but without actually running one, how could you possibly know? You can't hear all damaging sounds coming from problematic combustion events anyways.. Every stock FI '87-91 C/K/R/V on here is running one.
EGR: apparently TBI EGR (for trucks at least) is independant of the ECM, so removing it shouldn't throw a code.
Easy fix for the VSS is the '81+ cluster, I've got the one I pulled that has the VSS stuff if you are interested. (not like they aren't easy to find of course)
Wiring the ECM: you can cut a hole, or take the time to depin the ECM connectors, and open up the heater wiring grommet to pass them through. It takes just a few extra minutes (seriously) and is one less hole, plus it's chafe resistant. Depin the heater wiring to remove the grommet for mods.
EVAP and AIR are removable as well, dunno if that will throw a code or not, suspect no on the truck.
What year is the setup you have? (well, BCC will say which year too)
Oh yeah, and whats the BCC on the PROM? Pull the access panel on the ECM and if there is a carrier, eject it with the side levers (like RAM in a computer) and pop the blue cover off. Under the blue cover, there should be a 4 letter code, like "APYP". Haven't dug into TBI stuff much, not sure if the carrier/PROM setup is the same as TPI or not. But pulling the access cover off to look won't hurt anything.
I just checked out a TBI .bin (the "programming" for the PROM, what the engine runs off of, which is identifiable by the BCC sticker on the PROM) and there were conditions to enable AIR and EGR that you could turn off, as well as spark differences. If the .bin you have includes those conditions as well, you could potentially see some issues.
Doubt the chips themselves I have would work in your setup, but any mods needed for your setup I've got the software/hardware to do it, short of maybe the chips.