As others have suggested it is important to use thin layers. You can always add a second coat but it's tough to undo them. Heavy coats will result in waves.

Be careful if you choose to sand, I have tried this and if you nick the threads it's hard to fix cosmeticly. I ended up cutting the whole thing off and starting over.

Even the light version of Flex-Coat can go on too thick. I have trouble coating large areas evenly with a brush, you might find a mini-spatuala cut from an old phone card or butter tub lid works better. I sometimes hit the coated wrap with a heat gun to smooth out the layer. I can also use the spatula to remove excess.

I read somewhere that rod manufactors spin the rods as fast as 200 rpm when finishing. Since then I use my rod lathe to apply finish and it helps to distrubute it evenly. At 3 rpm the rod turner was too slow. Good for drying but not application.

I recently switched to a one part ureathane finish (U-40 Perma Gloss) it is about the consistancy of water and has less tendency to glop up. It takes a lot of coats but each coat only needs to cure an hour or so.

When all is said and done I am still trying to get that perfect 'dipped in water' finish I see on the best rods. But as far as I can tell the fish don't mind as much as I do.