[Low Elco]

Ummmmm... put the letters on over the final paint.
1. They're cheap vinyl; they tend to peel up and go chalky if left out in the sun, etc. Easier to replace this way.

2. It'll look cool right off, then they'll either off-gas and pop your clear, or shrink up and jack up your clear. You don't want no part of fixin this.

3. This is just me, but paint the gate and put one coat of clear on. Scotchbrite the clear. cut out the letters of the kit so you have the outlines with the letters. Lay them on, but use the outlines, and peel the letters out and tape up the gaps. Dust whatever color you want in here and clear 2x. Hey, you've committed "custom paint"! And they won't peel up or fade or look crappy! Ad if you screw it up, snad it off the clear and re-base! Who cares!

That's what I'd do, but I'm a shifty feller with questionable morals. Do what you Will!