The speed you are describing is when the 42RLE shifts back into 1st. It can be rough and most of the time you can clearly hear the transmission solenoids chatter as it engages. If you have worn motor mounts it could be making it worse. It will change the idle but shouldn't have a real effect on the brakes or vacuum unless you have a problem there. You might take a good look at your motor mounts and check the transmission fluid level.
Fair enough, I'll add it to the list. I guess I just wouldn't describe the shifting itself as rough though. Minus the ratio issues with with 42RLE + overdrive, I've found that it shifts fairly smoothly and consistently.