You'll only need to remove (or add) frame by frame if you're fixing a desync. If you want to remove a big chunk of sequential frames, just click on the first frame from the chunk, roll the side bar all the way down to the last frame, and click it while holding Shift.
edit:
here's the JoyToKey configured for the PS3 controller;
http://www.mediafire.com/download/9sp0pghdmx82va3/JoyToKey_en.zip
apart from the X, Square, Cross etc. buttons, here's the additional ones:
R3 = Save Current State
L3 = Load Current State
Digital Pad = Select States 1,2,3 and 4
Right Analog Up = V Sync Advance
Right Analog Down = Pause\Unpause
