I have been wondering whats best, what works long term for where ever fasteners go thru or set on the body like clips or screws. For instance the front edge hood trim on a 69 dart. It has screws and plastic clips. I know its likely to scrach or chip the paint where the screw goes thru, or even the nut may as its tightend up on the back side, or the clip itself could chip the paint. Then there are screws that actualy screw into the body like the spears on the rocker panels on the scamp. There are stainless philips screws on each end. What do you use to keep rust away?

There's lots of creative ways to keep rust away...Let's face it situations happen... The car is painted and now you've come across a hole that has too much paint in it and now you need to file it open for the screw/clip to fit... All you can do is open it up and use some paint for touch-up...

Some factory body screws have the ends dipped in wax to seal the hole...Some clips and fasteners have a "seal" on it being foam,strip calk etc...

In your example using the hood trim you first need to verify it'll actually fit the holes without chipping the paint first...If it's going to make it then use some strip caulk{I like the 3m brand} on the screwclip for the front then use some on the backside for the nut...Essentially sealing the hole from both sides...Then just peel away the excess around the nut...

On some super tight clearances you could use a gun/tube caulk but that would be a one time deal on the install and could get messy depending on the situation...And once it sets there's no going back for an adjustment if need be..

Humm, never thought of rope caulk. I have heard of using a heavy grease but didn't think that would last long.

Agree with Screamindriver:

I had a new set of Mopar running boards for a Ram and every machine screw in the kit had a clear, 1/8th of an inch wide material twisted on the threads. It was similar to that grey caulk strip you get in a roll that is used for sealing windows on houses.

Otherwise, I've always used a little shot of clear caulking on machine screws for putting on mudflaps and such.