No, the small drain holes had no plugs. I'd be afraid that plugging those would allow condensation to collect inside the hatch, promoting rust in there instead.

I welded the seams solid and then faired them in prior to paint.

How about clear silicone?

Hey Jim , nice job ! Pride of ownership shows !

I would not use clear silicone. You cause a paint adhesion problems in the future.

An automotive clear vinyl wrap or covering to the problem area,s of water pooling . http://www.invisiblemask.com/site.html?OVRAW=vinyl%20vehicle%20%20protection&OVKEY=vinyl%20vehicle%20protection&OVMTC=standard&OVADID=39677962011&OVKWID=151508345511