I'm going to be putting an accel base & SLP runners on the car at the same time I do the 165 ECM and harness swap. As long as I'm going to have that crap apart, I've considered getting rid of the EGR valve. What are the negatives to this? Emissions isn't a concern for me.

The EGR has no affect at WOT, and unless you would either burn a prom with EGR disabled, or would rather see the check engine light on all the time, I would just leave it.

I have an 87 GTA, I ditched all of my emissions stuff, EGR, AIR, Evap fuel, ALL of that crap, and NO check engine light(yet). That was 6 months ago! My benefit was a cleaner engine bay that I can work on, also had a bad EGR to start.

I'll be burning my own PROM. I'm not tearing the top of the motor apart to do a 165 ECM swap so I can run a stock chip.

I'm fully aware that I can disable the EGR in the PROM, but before I go ahead and do this, I want to find out what effect it will have.

the egr valve enables you to run more ignition timing and a leaner mixture at part throttle. unless you retard the timing alot you will need to burn a new chip. your gas mileage will suffer, and you wont be able to run as much timing at part throttle due to higher combustion temps. personally i think it is a mistake to take it off. it does not function at full throttle anyway, so it isnt hurting your maximum power output.

My EGR was stuck open a little, so I shot it in the vacuum port with some compressed air to close it. I disconnected it and disabled it in the ECM.

A WOT 1/4 mile run showed that in first gear I knocked so bad it retarded my timing 7.4 degrees. So I'd say, in high load/low rpm situations, expect some timing retard if you take your EGR off.