I know this is not the answer you are looking for, but I use the EHX Black Finger instead for this purpose.
I haven't tried the English Muffin, but judging from the demos it has a more bright sound than the Black Finger, I realize though that you get a wider range of distortion as well as there's an EQ on the EM, that you don't get on the BF.
But honestly, the Black Finger run as tube preamp or overdrive unit instead of compressor as it is intended as, sounds awesome.
You just put it in Lamp and Normal mode, turn down the amount of compression to just kick in when you are digging in deep and hard, dial in your Pre Gain (gain) to your desired amount of breakup/overdrive (or keep it low so that you only got the tube color really, and then adjust the Post Gain (level/master volume) to match or slightly boost your unaffected signal.
Eventual place an EQ pedal of your choice after the BF and you got all the EQ options you need.
Personally I run it at just around breakup point, so I got my tone going from clean over slight breakup to light overdrive, over a pretty wide spectra of tones in between, depending and accordingly to how hard I pick.
It is super responsive to your play and has a nice natural deep sound.
I at least don't use any form for EQ with it.
It is in the same EHX series as the English Muffin, which means it has 2 high voltage preamp tubes, run at 300V each, equipped.
And the BF is basically a tube preamp with a tube input and a tube output stage, just with an optical compressor circuit in between (which can be almost shut off), instead of having a Marshall amp emulator circuit like the EM build in.
I am not saying you shouldn't go on with the project of modding the English Muffin to work better for bass, I am just saying that for me the Black Finger already works as it is, and maybe it would for you as well.
Worth considering at least.