Do I have to sand epoxy primer before appling the filler... is it a chemical vs a physical bond ?If so what grit ? Thanks

Yes you MUST scuff once its completely dry.
Scuff with green or red "scuff" pad or 220--280 dry paper.

If you missed the time window (should be listed on tech sheet) then,yes, you must roughen it up, I'd use 120 grit paper,

yes that is what I was getting at. The window is 72 hrs before requiring sanding..but then started to wonder if the epoxy is NOT completely dry then maybe it wouldn`t be wise to put the plastic on ??

As long as you didn't hose it on too much and now it's thick and rubbery,you'll be fine,but if it's thick, I'd let it cure for a week or two, since you missed the window anyways. Roll it outside everyday and let it sit in the sun.

I never started yet. I had intended to use the epoxy for adhesion and rust prevention in the area requiring a skim of filler. But was wondering if the bond with the primer{semi-smooth }within 24 hrs would be ok or would it be better to leave for 3 days then sand {roughen -up and apply filled then ? Thanks

Check the tech sheet, it should tell you how much time you have before topcoat, I believe the average is 72 hours