If you have a set of calipers and a straight edge you should be able to get an idea of how space you have. The other option is to build up one cylinder with the heads and valves on, but no cam. Put some clay in the area where the reliefs are and turn the engine over once. (BTW - leave the spark plug out so that it will turn). Alternatively you can put the piston at TDC and the using a micrometer measure how much each valve can move down with finger pressure.
I doubt that the difference in CR will make a huge difference to the MFI -- I suspect that you could adjust around it using the part throttle adjustment. If you were to use carbs, it should be even less of an issue.
Here's a thread that contains a lot of different weber configurations. If you look at the successful combinations, I'm somewhat surprised by how they don't vary a whole lot.