Well...
There is a small increase in temperature due to the airflow over the radiator being blocked, but that is offset by the heat load taken off the radiator with the external cooler - and then some. You'll be coming out ahead on that score.
I've always preferred to plumb the cooler separately from the radiator, and just leave the internal cooler disconnected. There is a slight issue with some transmission taking longer to reach operating temperature, but my 87 didn't seem to care. If you are worried about this and haven't bought your kit yet, there are a few with a "thermal bypass valve" that will recirculate the fluid, bypassing the cooler, until the fluid reaches 190* and then open to cycle cluid thru the cooler element. As I recall, these valves also "fail" to the open position, meaning that the cooler will be in circuit if the valve decides to quit working.
Either way, I've always thought that the benefits of getting the internal cooler out of the circuit and cooling the engine offset the slight disadvantage of the transmission taking longer to cool - and the availability of the thermal control valves has solved that problem as well.
While you are doing the cooler, do yourself a couple other favours -
Check your speed shop for M14x1.5 to -6AN adapters, Russell and Aeroquip both make them (and I think Earl's does as well.) This will allow you to get rid of the silly little "Ford-style" QD fittings and use proper plumbing. The OEMR fittings for QD are M14x1.5 threaded, so these should work. The houses will have them in aluminum, but I'm working on a batch in brass. You'll be able to use "push-in" -6AN fittings with regular hose - just make sure they're compatible. A speed shop can help you with that.
Add in a "remote" spin-on filter so you have proper filtration for your transmission. The AW4 "filter" is usually just a metal screen, and won't catch much. Mount the filter boss so that it will be open end UP, and remember to fill the new filter before you put it in to minimise "dry time" when you start after your oil change. Plumb the filter between the transmission and the thermal valve.
I didn't look to see where you were, but I'm available for assistance if you're in the Bay Area...
5-90