>>28525811 (OP)Pad slapping is a meme. Change Pads and Rotors together, grease your Slide Pins (assuming you have a sliding Caliper), take the Shims for the Pad Ears off and Wire Brush any Rust off where the Shims sat on the Bracket.
Finally, go for a drive and do at least 10 hard (but not ABS) stops from like 40 down to 10 MPH. Wait at least like 30 seconds between each stop so the Brakes don't overheat. You're trying to bed the new Pads into the new Rotors, not cook them.
As for your Tranny issues, hard shifting is usually attributable to putting the wrong type of Fluid in.
If you had said it felt like your Tranny was slipping, that would've meant you waited too long to change the Fluid and now some of your Clutch Material (yes, Autotragics have Clutches) has worn off the Clutches and is floating around in the old Fluid that you drained out.