I've just completed my best looking built rod to date, using two very thin coats of Flex Coat Lite on the wraps using Walmart's Plaid shader brushes suggested from this website. After curing the wraps look as though they could use a 3rd coat since there are a few slight thread grooves still showing. I'm debating whether to put on a third coat of Flex Coat Lite or would using the one part Permgloss be a better option? I read some horror stories where one different finish seem to attack another. What's the best way to put on a third coat and since the wraps have cured for just over a week, should I try to rough up the wraps with ScotchBrite or something like that? Thanks.

I use permagloss over flex coat routinely. It does not attack it. If you go with permagloss, you shouldn't have to scuff the FC. If you go with another coat of FC, then scuff what is there.

You can also just use a 3rd coat of FC lite. A trick to get a thicker coating from FC is to mix the finish and let it sit for 10-20 minutes (depending upon tempreature) The wait will allow the finish to become much thicker, like a normal weight finish.