Just to be clear, the problem is that you have some stripped bolt holes in your tractor frame, and you want to secure the loader frame to the tractor frame permanently with welds?
I think you're trying to avoid welding out of position by only putting a single bead on the top, but I do have to wonder whether a single bead will provide enough strength to replace the missing bolts. It's surely not how a manufacturer would have welded it up.
Bolt #3 will be grounding the two pieces together. Wire wheel where you are going to weld. The powder coating will be slag when you run the weld. Another method would be tapping the existing holes for a bigger bolt. If bolt #3 has questionable threads; do the first holes and then back #3 out and do that one oversize also.
I think you're trying to avoid welding out of position by only putting a single bead on the top, but I do have to wonder whether a single bead will provide enough strength to replace the missing bolts. It's surely not how a manufacturer would have welded it up.
I have to agree with Josh that only welding the top will not be strong enough. Are these blind holes or can you drill them through and use a bolt and nut to hold the frame on? If something goes wrong with the tractor and you have to split it, would this frame prevent you from doing that?

You guys think it would be a good idea to weld the entire perimeter?
From:
Tap and die - Wikipedia, the free encyclopedia
Bottoming tap or plug tap
The tap illustrated in the top of the image has a continuous cutting edge with almost no taper between 1 and 1.5 threads of taper is typical. This feature enables a bottoming tap to cut threads to the bottom of a blind hole. A bottoming tap is usually used to cut threads in a hole that has already been partially threaded using one of the more tapered types of tap; the tapered end ("tap chamfer") of a bottoming tap is too short to successfully start into an unthreaded hole. In the US, they are commonly known as bottoming taps, but in Australia and Britain they are also known as plug taps.
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I would think the larger problem would be welding to the tractor frame. They typically don't make this out of mild steel, and it would take specialized knowledge of the material to weld it, if at all.