Hello badriand. Welcome aboard.
The original nuts for those cowl to floor connections were held in place and I don't see that they were ever designed as an adjustment point. Although, I know the height of those blocks will affect the door adjustment.
My original wood blocks were rotted and partially collasped. I replaced them with 1 1/8 inch thick dense rubber blocks shaped as the original wood.
That connection could be welded. It's probably only there because of ease of manufacturing, IMO.
I think fitting the doors before welding would be prudent, if that's what you decide to do.