Stovebolt frames were designed to flex a little. Welding crossmembers in will create stress risers and cracks in a very short time, as well as causing changes in thre metallurgy of the frame in the area of the welds. I'd leave well enough alone, and do as good a cleanup as possible without removing the crossmembers. I think you're about to open up a very costly can of worms.
Jerry

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