You have a dog fish.
We like it.
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If the pin holes are down to clean metal, couldent you temporarily tape it from behind and fill the pinholes w JB weld? Then use epoxy primer over the top to seal them in?
I'm a big fan of Rustolem Rusty Metal Primer.
I've always used that and not any of those "reformer" products or coatings.
I would strongly suggest Lord Fusor Crash Durable Adhesive for putting the new cowl top on.
No welding and you won't have any area for moisture once you get it on.
If you weld it, there will be areas that will have the paint burned off.
Someone has a thread on here doing that.
Cowl Rust! What is the best way to fix it?
I've done it too.
I had similar pin holes around the stand pipes and used polyurethane sealant on them.
No point in welding them. Who is going to see it anyway?