You are going to enjoy this boat, looking real good. As for the CG do worry to much about that. As you know with the water prop boats, most start at 30% but on the airboats, thats a all new set up, since there is so much leverage up high. Your engine may be a tad on the back side, but again don't worry to hard. One of the main advantages to the airboat is again the leverage the engine has. At worst, if the engine was to be set level to the hull, you may have some hop. When you set your engine mounts, just set the rear mount a little lower than the front, 1/8" to around 3/16". It is a good idea to have slots where the bolts hold the engine mount, so that you can adjust as needed.
Not to sure about needing longer bolts for the new jug. There is a shim that fits between the jug and the crankcase, and it is less than 1/8" thick.
Your on the right track for the rudders, 14" tall X 2-1/2" wide. Regurlar cabinet door hinges work fine and you can still use shims to get the correct pitch and toeing that may or may not be needed. You will have to run the boat first to see if rudder adjustments are needed.
Another thing that you may want to do before decking. At the transom to bottom, this area takes a lot of abuse and it is the main area that may pop loose, it will not hurt anything to add a little extra epoxy or laminating extra supports.
Your boat is looking really good, and you should be race ready in no time at all.