Dan,
A very professional looking job. If you are ever looking for some side work, I think that ERA would hire you
Not a simple job to have to adapt what you receive, but as you say, it is doable. Looks pretty smooth now.
Not surprised that the top gets a little noisy at about 50 mph, they are not meant to be a permanent top; just something to keep the rain off of you in a downpour, and then stowed in the boot.
I had someone suggest to me that getting in an out of one with the top on and side pipes can be a little tricky.
I ordered a tonneua cover from ERA and it should be here in a couple of weeks. I am going to start with that before I move on to the top.
Maybe after you are done in PA you could swing by upstate NY...there is plenty of room at the inn