4Runner,Changed brake master cylinder, bled 10 times, and the pedal is soft The rear brakes are not locked but close. Truck now running rough.

I changed my brake master cylinder on a newly purchased 1997 4runner due to a soft pedal (no leaks) and bled the brakes 10 times. I bench-bled the master cylinder and had no issues with the install. Saw a video on YouTube that said to run the vehicle to speed and jam on the brakes, thus pushing any air down so it could be bled. Did this in drive and reverse. Brakes made a strange noise when jamming on the brakes in reverse. Now the brakes aren't locked, but not free and the truck is running rough. No issue with the engine idle or rear brakes prior to replacement of MC. Bled the rears and t