good start! I think what you will benefit the most from is just getting some prototypes cut out and actually testing them. Also figuring out first hand how moving a shock position or a link position really effects the handling of a crawler.
One piece of advice that i will offer (and i don't know if it is correct but it is my personal preference and as a science minded guy, i feel like this should be the way all chassis are)...
I like when changing a mount position will ONLY effect one variable. In science when conducting an experiment, to have complete control, you should never alter more than one variable at a time. So on that note, For the MRC, their is only one option for mounting shocks and links on the axles. And the way your chassis mounts are set-up (and a lot of mounts on after market chassis are this way actually), is that the mounting points are at all different distances from the axles mounting point. They will always be all different distances as long as the mounting points change in a straight line formation. This means that more than the geometry will change when making adjustments. For example, as you mount the shock further in the chassis, your geometry will change (good, that's what you want to happen), but your ride height will also change because the shock is mounting deeper (bad, for one because then you are messing with two variables at a time and you should really only change one variable at a time to dial in your performance, and two because if you feel the need to change the ride height, you can do so by other means dedicated to changing ride height, such as changing shocks or adding spacers to your current shocks). For the links, changing mounting position will change geometry (good) but will also change the caster (pinion angle basically but more technically and equally important, it is the angle of the steering block when look straight at the face of the wheel) because mounting the upper link further down effectively pulls the axle in but only at the top so it is actually rotating down and bringing the pinion angle down (bad).
For both these issues, there are two solutions:
1. everytime you mount your shocks or links to a different hole, you change the length of the shocks or links to compensate for loss or gain. This could get very labor intensive if you change your mounting positions often or at least a few times to dial in your rig. It could also get spendy if you end up needing to purchase longer shocks or links to maintain the current dimensions.
2. When designing the chassis, design it so that changing mounting positions will only alter the geometry. to do this it is very simple and to me it takes out some of the guess work on mount positions. In your cad program, locate the mounts on the axles. draw a line that is the VIRTUAL length of the shocks or links when viewed from the side. (when viewing from the side, a line that is parallel to your eyes, it appears to be the real length. But notice as one end of the line gets further away or closer to you, it appears shorter (talking 2 dimensional here). This shorter length is the virtual length. It is important and hard to understand why without getting hands on or just being very geometrically minded.) Anyways, the virtual length is easy to find in CAD by drawing an isometric drawing (a top view of the links transfering to a side view.) Next take these lines that represent shocks and links and "mount" them to the "axle" in CAD. Always keep them there and just rotate them slightly and mark each point as the top of the "shock" or end of the "link" changes. These are viable points for mounts. You will end up with arcs (one for the shock and one for the link) with the centers at the axle mounts and the virtual lengths of the shocks and links being the radii for these arcs. You should only have one arc per shock or link. You can also get close to this method by placing mounts along a tangent of these arcs (some designs do this) and you will minimize other variable changes. But while you are in CAD, you might as well just draw out the arc and ensure that your axle will remain in it's original position throughout changing mounting points. Now this is all considering you neglect how the shocks will change behavior as their angles change

haha but that would get into some intense calculating that i don't know about and probably wouldn't offer very much if any improvement.
So that was long winded but it is a concept that is very helpful to me and i think it should be helpful to you if you can make sense of my ramblings. haha. So much of this stuff is visual and hard to explain in just words. good luck! i'll watch your progress and chime in when i can.
EDIT: one more thing. consider weak points such as near holes. For small holes like for 4mm or 3mm or 2mm or whatever size screws, i generally try to make a ring of material around the whole that is equal to the radius of the hole. For autocad, it's easy. Just draw the mounting points, offset all the mounting points with a distance equal to the radius, connect the tangents of these circles around the mounting points, trim circles, fillet corners, cut out unnecessary material and voila!

Also braces between the tops of the two plates is important (as stated by someone previously). The stock skid is not very rigid and the plates will flex too much.