My understanding of the Great Loop is that it is almost all rivers, canals, and the ICW - in other words, protected waters. So I think there are certainly good contingency plans for a C-22 in foul weather or other threatening conditions. I can speak for the Great Lakes legs - you can do it with careful attention to weather forecasts and radar on an iPhone or equivalent.
On the boat mods, I would go for an expanded pop top or pilot house behind the mast, more to avoid complexity, and real mast support issues if you move the step up 20 inches.
All the accounts I have read of the Great Loop (and my own experience in canals and the ICW) imply that you will do a lot of motoring, so make sure you have a good set up for motoring. I recommend a tiller pilot especially for the open water legs in the Great Lakes, Chesapeake, sounds, etc.
You know your boat, and if, for any reason, you decide you have had enough, you just need to get to your car and trailer, and call it a day!
I say go for it! Fair winds and following seas, and we will help any way we can with your specific mods - just ask as you know your decisions, and designs.