Ended up painting under the shrink rap using Perfection and with good results. The next season I painted the flybridge but not under shrink wrap. Had one coat ruined by the weather. Debating about wet sanding as I have a few spots that need attention. Overall I am happy with the results and moving on to the next project.
Used a different painter to paint the flybridge and put two finish coats on thicker than I did. More drips and sags than I had but they wet sanded and compounded out nicely. When he went to wet sand the the pilot house that I did he blew through in several spots so he stopped. Compounded the rest and it turned out nicely. He is going to spray another coat or two on the area that went through to the primer and blend. Interlux does not suggest wet sanding so if you use thin coats just compound.
Have used the original shrink wrap for two seasons but had a large rip as I did not support it properly from inside the second season. Will patch and use the same frame I used the first season and get another season out of it.