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These days with all the different paint chemistrys it is best not to mix them haphazardly or bad things can happen. Paint is expensive, and requires a lot of labor, the last thing you want is to have to sand it all off and start over!
Start by selecting the brand and type color paint you want to use for your final finish, then stick with that brand and system's undercoats all the way back to the DTM (direct to metal) first coat that is recommended by the manufacturer. Use their recommended thinners as well. Unless you are planning on using just a cheap single component implement or hardware store all purpose paint such as Tractor paint or Rustoleum, make friends with your paint supplier and take his advice. He is not there to sell you the most expensive paint he can, but wants you to achieve a trouble free paintjob, and knows what is needed to obtain it.
Check with the manufacturers recommendations, but the rule of thumb is never put polyester products (ie: body fillers) over etching primers. So it you have any filler work to do still, use epoxy instead over bare metal. Don't trust trying to sand off etch primer to do filler. No matter how clean you think you have it, there may still be enough to cause peeling and failure later. Prime with something else first (epoxy or urethane) before applying any body fillers. And as others have noted, unless it's a professional use-designed product, rattle can materials and the "good stuff" don't mix.
Etching primer is old school...stick with a Direct To Metal (DTM) primer and you will be fine. I have used various products but my current favorite is SEM Metalock...it works as a DTM primer (high build), a surfacer, and a sealer. I find it very easy to spray and to sand. It holds up well under various basecoats and single stage paints. I have left primered parts sit for years without any rust through. Give it a try, you won't regret it. http://www.semproducts.com/product-c...-build-primer/
I have to agree with Charlie on this one. Self etching primer usually contains phosphoric acid or some other acid base to etch the metal. Etching is really a nice way of saying to form an oxide layer which is generally more porous than clean metal. The paint will bond to the etched metal. The problem is that when applied, the self etching primer relies on moisture in the air to react with the acids. If you spray in winter or in a dry climate the acids won't fully convert. That leaves behind the dry acid traces in the primer. Those can be conductive, so the result is that in some climates, you could get a conductive path for galvanic corrosion to happen under the paint.
My theory has, for some time now, been that if you want to do a surface conversion to the metal, etch it with an acid wash, then rinse it with clean water....then let it dry completely before applying a primer.
With modern paints, as Ax says, talk to your paint supplier. Make sure that the primer you apply is compatible with the topcoat that you plan to use. Most two part epoxy DTM primers will stand up to most of the topcoats. The manufacturers call it a "paint system". In my opinion, it is worth a lot to know that the primer won't bubble off when you're spraying on your expensive topcoat.
Etching primer is old school...stick with a Direct To Metal (DTM) primer and you will be fine. I have used various products but my current favorite is SEM Metalock...it works as a DTM primer (high build), a surfacer, and a sealer. I find it very easy to spray and to sand. It holds up well under various basecoats and single stage paints. I have left primered parts sit for years without any rust through. Give it a try, you won't regret it. SEM Products :: Metalock DTM High Build Primer
Thanks for the lead Charlie, looks like the best way to go.
I will be sanding off the etching primer on the 2 rear fenders, do you think I will have any issues with these when I spray the metalock on them?
You should not have any issues with spraying the Metalock over the etching primer...in fact, this DTM primer is suitable for application over most any prepared surface including OEM paints and fillers. The instructions call for a "straight from the can" mix of primer/hardner (4:1) for use as a DTM high-build primer application but you can also use it in a 4:1:1 ratio for surfacer/sealer apps. This is when you have filled and sanded the intial primer and now you are ready to apply the final primer coat prior to final sanding and color coat. I use it as a sealer and apply it over the entire surface just prior to basecoat application...no need for additional sanding or prep, just let it set up and flash for about an hour and you're ready to paint over it.