Hi Mike,
You have raised some good questions - some of which I had to address when I built my obs. I did a lot of research on the internet - particularly of construction articles - to see what worked and what didn't for others.
Do you think that 41 m/s is high enough for your location? I designed for 160+ kph here, where gusts are the killer.
To address some of your Qs:
1. It's most important, especially when you start imaging, to have the pier mechanically isolated from the building/slab. You won't want movement due to foot traffic or wind gusts on the building transferred to your scope. So you need to design a physical gap between the two. I poured a reinforced block in the ground first, then poured a slab over it but not touching it. The concrete pier was poured soon after, and is connected to the block. There are some pics of it here in this thread
http://www.iceinspace.com.au/forum/showthread.php?t=36222&page=3
2. To figure out your pier height you need to work backwards from your final set-up, so that you're sitting at a comfortable height when observing. I have not had experience with a GEM, but no doubt you will need to cater for variable observing heights (adjustable stools are great for this). If your walls are 2.4 m high, I would suggest that you might need a taller pier - it's occasionally good to be able to view the horizon. I have catered for future upgrades by installing a solid concrete pier to a certain height, and then bolting a steel pier on top, so in the future I can replace the steel pier with a different length if necessary.
3. You can get drawings of some mounts' bolting arrangements from the net. (Eg. the AP 1200) Since I made a sizeable pier, I spaced eight 1/2 inch studs around top of the pier so that the steel pier's bottom plate would be securely connected.
4. Since you're planning to install some solid gear on top of the pier, you need to design it so that the pier won't be a weak point. That is, you want it to be very stiff. There have been a few threads on IIS discussing the merits of concrete vs. steel, and it seems to be almost a personal preference ultimately. I have used both - as I mentioned above - and my pier is quite tall as the scope is on the second story of the obs. So I used a 457 mm dia former to pour the pier. For a GEM though, you might need to be careful that an excessively large pier did not foul the couterweights!
Finally, there have been a number of excellent roll-off-roof observatories described on this forum for starters.
Good luck with the design!
Chris