ICE-32 is a performance treatment. Going by what a guy I spoke to said, it's not detrimental in any way like a leak sealer or something along that line would be, though I suspect you'd be paying extra for it and as I mentioned earlier, I can't tell much difference in my two A/C systems, one with it and one without (FWIW, I've bought straight PAG-46 oils at both NAPA and at Carquest).
The deal with flushing the muffler is the same as for a serpentine-flow condenser, it's virtually impossible to get all of any debris particles out of one, so replacement is a better option. Though if the system is clean to begin with, then there's nothing to worry about.
All the fittings use o-rings, or in some cases are a compression type fitting. Thread sealer would do all of nothing for it, but could gum things up. Best thing to do is replace all the o-rings with new ones throughout.
As for the oil in the evap coil though, that one I'm not so sure on... The Ford manual says if you replace the evap core for any reason, to put 3oz oil into the new one to maintain the correct oil charge in the system. I would think that would mean subtract 3oz in your case, though I wouldn't feel comfortable with it myself (maybe blow as much oil as you can out with an air compressor (maybe flush some lacquer thinner through it at the same time) and then just add the full amount of new oil on it).