You can just stick heater hose caps, vacuum caps, or something like that on there - but you shouldn't get too much leakage anyhow.
As I recall, the OEM Auxiliary cooler works in concert with the internal job, but I've not had any ill effects from bypassing the internal cooler entirely. I'd like to do the job right on the next few I do, and get a thermostatic valve (bypasses the cooler until a certain temperature is reached, then includes the cooler,) and continue NOT using the internal cooler - since you'll get slightly more efficient engine cooling as a result (even with the transmission cooler in front of the radiator, you're not adding as much thermal load to it as you are with expecting the coolant to cool both the engine AND the transmission!) I think B&M & Trans-Dapt both make kits including those valves, and they probably sell them separately.
I'd tell you what size caps you can use, but I've long since converted to -6AN, and just use -6 caps and plugs when I have to service the thing...
5-90