i'm at work right now and a little slammed so i can't reply in too much detail... i'll try once home.
yes i've used potting coumpound. none purple and maybe that's the problem. i fin the stuff is absolutely horrible to get off. all gooey like. even silicone is easier to remove... and that says something. one option is non conformal sealer also.
i have done a number of fuel injection conversions over the year using motec, haltec, holley tbi, and one electromotive. i am in no way trying to disuade you. if you have a strong electrical and injection background (which from the sound of it you do)... i say go for it!
know the limits of the system. speed density systems like megasquirt do require a fair amount of pre-tuning to get going, and also require a certain amount of maintenance to keep alive.
when running well the injection will knock the pants off any carb. hands down.
post loads of pics and info as you go.