I'd leave all the holes you can tell are factory.
In my mind you're supposed to see holes in a big truck frame, they were there for other options or configurations, it's expected. What might look wrong is a completely slick frame with no extra holes. And you'll find some of them handy for other stuff as time goes on.

Probably leave any non factory holes too unless they just look wrong. Any holes in the frame you don't like I probably wouldn't weld them though. Small ones can be tapped and screw a bolt in, trim off the ends and peen and grind it flush. Larger ones you could use some JB weld sort of stuff if you really wanted to (probably not ideal but safer than welding a lot). Also consider dressing any buggered holes clean with a slight chamfer so they look good/factory.

Grigg

•1951 GMC 250 in the Project Journals
•1948 Chevrolet 6400 - Detroit Diesel 4-53T - Roadranger 10 speed overdrive - 4 wheel disc brakes
•1952 Chevrolet 3800 pickup
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"First, get a clear notion of what you desire to accomplish, and then in all probability you will succeed in doing it..." -Henry Maudslay-