I'm not sure, but I think your problem was mixing different lubricants. The transmission would not like that at all. It is a bad practice to do that, and I think you just learned why.
Don't bother with the last cup or two of fluid, it won't change anything except how long it takes to add the full quart.
You have far more serious issues than being a cup low on fluid. The most critical issue is that you did not flush the transmission at all.
Please tell me that you did not reuse the clamps. Please! Those clamps are one-time use only. If you have to take them off, they should be discarded and replaced with a standard hose clamp, or another clamp like the one you just tossed into the trash -- except you didn't toss it, did you?