justinh said:
I cannot however get a allen wrench onto the screw/bolt that attaches the top chamber to the bottom chamber due to the shock blocking it.
You should not have to remove the stock shock absorber to remove the stock mufflers.
Having done this a couple of times, I think the problem you may be having is that it is difficult to get sufficient leverage on the short-end of an "L" shaped Allen key to release the 6mm hex cap screw that holds the upper muffler to the bottom. I recommend that instead you buy a 6mm hex socket and use a long ratchet extension to get down into the gap between the inside of the muffler and the outside of the shock. Ideally you want a long-shaft, ball-end metric hex socket - but unless you special order it these are hard to find, so stick with the standard length hex socket and use an extension bar.
If you don't have (or don't want to buy) the socket, it is possible to use the L-shaped Allen key, but to do so you need to get a box-end wrench and loop the closed end over the short arm of the Allen key to get enough leverage. I've used this method in a pinch - but it is almost guaranteed to either skin your knuckles or strip-out the head of the hex screw.
There are plenty of other 6mm hex fasteners on your V-Rod, so buying the hex socket is a good investment.