I am planning on removing the first two diodes and I wa wondering do I just cut them out or do I need to solder in jumper cables and what other mods would make the muff sound a little smoother and fuller sounding thanks.
Well, looking at a schematic of it, you prob. will not get more drive. The diodes in different orientations is what achieves the signal clipping(distortion.) It will be more mild taking those two out.
You'll get a bit less fuzz, but more bass and more volume. It'll sound more like a Colorsound Supa/Jumbo/reissue Tone Bender which is just a Big Muff circuit with the first set of clipping diodes removed, and in the case of the jumo and reissue, the post tone control transistor stage.
try this - remove all the diodes and replace one section with a pair of LEDs AND you should increase the treble side cap from 3.9 nanofarads to 5nf - this will smooth the mids out a little while keeping the highs giving you more low mids. and replace the resistor in the tone stack going to the ground with a 100K resistor - if not already. you'll end up with a VERY huge smooth sounding big muff after that.