Auto to manual question. (Wiring specific)

[Redneck_toy]

Hey guys, I have a quick question for you wiring gurus for the 4l60E. Long story short, I swapped an SM465 into my 94 a few months back. I recently built a vortec tbi (tbiparts.com recipe) for the 4l60.
Five months later, I swapped in the stick. Everything runs fine, except for the pesky check engine light that comes on after the truck has run for 30 minutes or so due to the computer still looking for tranny feedback. Kill it and restart, light goes away. I talked with Brian at tbiparts, and he is more than willing to reflash my prom to turn off the tranny for a modest fee. My problem is this - if I send this prom out to be refreshed, the only other chips I have are the original from the truck (auto) and the chip from the 92 from which the tranny was pulled, both of which still have the egr active. If I put the stock chip in there, I'll be running in closed loop all the time due to the egr, correct?
The question is this, is there any tranny wiring I can ground out, or add a diode or the like to cancel the tranny CEL? Or, should I just put around for a few weeks in closed loop with the older chip in place while the new one is being reflashed?
What's the concensus?
Thanks for the help

 

[Redneck_toy]

If I understand the egr circuit correctly, it is only active during deceleration at higher speeds, but am uncertain if this is enough the make the computer stay in closed loop if it is removed. I know that using these engines in a stand alone configuration for an offroad only rig, you are able to ground the egr wiring to eliminate the CEL, buy not sure if it stays in closed loop or not, since it isn't near as important at offroad speeds. If I need to post in a different thread, let me know.