Excellent info. I didn't quote the whole thing, but there is a wealth of info there.
Do you have any thoughts on the gasket materials - what to use/what to stay away from? Or are they all comparable?
For the top of the transmission case the FELPRO KARROPAK material would work fine, being nothing there is pressurized. Thickness would be determined by the thickness of the original gasket they make it in several thicknesses. 8-10 years ago, I bought a cheap digital caliper for lathe work, really handy for measuring other things like gasket material. That one gave up the ghost on me this winter and got a new one at Menards for around $20 just like it. Don't use it that often, but nice to have for things like this.
I ran the part number for the aux. hyd. control gasket through Bane-Welker/Circleville and shows the price @ $1.87. You may call Plain City and check that price. If it is, I'd get it through them. When it comes to hydraulic pressure, I bite the bullet and buy the OEM gasket. When I typed in the 3061055R2 P/N 3061055R3 popped up too, that one shows $30. Not sure what the difference is other than being made from a different material..?? A parts person worth their salt may be able to answer that.
I suppose silicone would work there and be much easier. I will just say I have bought more than several tractors/garden tractors to add to the collection here where a PO has used it on engine oil pans, transmission covers, and anywhere else you can use it. Apparently, their thought was if a little does a little bit of good, a lot will do a lot of good. A Farmall B I bought years ago someone had used it on the engine oil pan, had the little blobs sticking out on the outside, and was seeping. I pulled the pan and had blobs on the inside too, and some had come off, apparently washed off from the oil splashing around, it had about 1/3 of the sump screen covered. Luckily it didn't starve the engine for oil, and I just hoped the filter caught anything that may have passed through. It was the same with the gear shift cover. Flushed that well and got it cleaned out. Don't know about the long term, someone made me an offer I couldn't refuse, so the little B went to a new zip code.
This was back from the day of the "blue goop". Seems everything I've seen it used on it wept a little oil after a number of years. That may have had something to do with surface prep, not sure. I'd suggest just use what feels right for you.