Blimey oh riley, that was an expensive MMR!
q1 - Leave it as-is. For starters, the max is 33.33MHz as I recall... The RAM doesn't autoconfig: you have to specify the speed of the RAM via a utility (CSA-MMR). I don't think it supports speeds other than a few predefined numbers, however I'll check tonight
q2 - There are jumpers to configure the wait state that you need to set on the daughterboard. I think it takes care of all this and you don't really have any options.
q3 - I have exactly the same desire. My thought is that we'd have to decompile what the SROM option does within the CSA-MMR command and rework that to load 3.1 off a file. Or some other location... There has been mention of a utility that might be a step towards this called "MMRBoot" on c.s.a.hardware, however I've never found any reference to it apart from one post.
q4 - It might work, however there's talk of AdIDE being incompatible with accelerators (ref amiga.resource.cx...)
Other comments: you will have to do something about the floppy drive in the 1000, as the MMR will physically interfere with it. My plan is to use a 600/1200 drive in there, but I'm unsure of whether this will work. The back up plan is to build a small adaptor which shifts the MMR back by a couple of inches - I think jeff has done this and there's pictures on this very board.
In fact, I think Jeff has tried an accelerator with a 68k CF adaptor...
The decompilation of CSA-MMR could be interesting and could be the best route to 3.1 on there. At least there's two people in the world with the same ultimate plan!
BTW, Mika (the chap who makes the CFIDE68K) has plans for to make an expansion port mounted version like this (but smaller):
http://www.amiga.org/gallery/index.php?n=2549=6 - I'm pestering him politely as this would be perfect for me!