I don't like internal tom mufflers. They don't work well... the head goes down and they poke up. But I too like the looks of them and have taken them out of Gretsch drums, taken them apart and just put back the knobs with nuts on the inside just for looks. You don't have to alter a drum that came with them to do that, the only thing is that the threaded rod of the tom/snare mufflers (on mine anyway) was crimped at one point so it couldn't be unscrewed all the way, and when you do remove it there will be some thread damage. I never tried using a die on the threads first. I know that is monkeying with the originality and I'm nervous of that.
I'd probably pass on the kick muffler as I like the old external types, blankets and pillows and such. The JP stock Gretsch one is a cool unit though.
If you do mount any stuff, make sure the drilling is as perfect as you can get, use new or near new drill bits etc and I wouldn't attempt it if I was in the slightest not 100% confident I could do it and wanted it.
The whole thing is the kind of decision I'd want to consider for quite awhile.
The problem with the Gretsch bass drum mounted cymbal holder is that it's archaic. I've heard some people modding it with a memory clamp and as the diamond plate is easily available I'd probably do that. I like/need that type of holder. Make sure you get the right diamond plate - the earlier ones had exposed screws, the later ones (from the end of the 50's, something like '58 someone please correct me) have hidden mounting posts cast in the plate itself.
The stock Gretsch/Walberg tom holder diamond plate, the part that mounts on the tom, is semi-lame as it doesn't swivel... I'm not big on the rims mount looks (I'd have to say there is, to my ears a sonic difference though) but they probably would get the tom where you want it more than the Gretsch. But the Gretsch is livable.