I have not built any 250Rs with 400 Pilot cylinders nor do I think that I could build a lower end for one that I would want my name on. I have rebuilt a few that were done by other shops and did not like what I saw. There was a lot of welding on the cases that was needed so that the transfers would match up and for the relocation of the studs. The welding warped the main bearing pockets, cranks seal pockets and the case halves mating surfaces. I think that I could do a lot better job of welding but there will always be some distortion no matter who welds it or what type of welder is used. Welded cases will never be as strong as the original cases.
The 250 R crankshaft does not have enough mass in the crank webs to make the ports work optimally without having to do some really radical things to the ports.
I believe the 250 R crank web diameters are too small for the stroke that is necessary. The distance from the crank pin hole to the outside of the crank gets too thin to be able to put the interference fit that is necessary for a crank not to flex and crack in that area. Welding the pin does not stop the crank from flexing in this area it just keeps the pin from moving in the crank pin hole. I have a few customers that have had their cranks stroked to 77 to 80 mm and have not had the crank pin hole crack or the welds break but these were not high HP engines with much time on the crank. With the limited amount of room in the cases and the large number of split crank pin holes i have seen, I do not plan to start building stroker cranks or stroking existing 250 R cranks that are destined to premature failure.
I would keep your 350 and get with a motor builder that can give you a good engine combination (ports, pipe, head, carb, etc) if you want to make some respectable power. I would not trade what you have for the 400 pilot cylinder engine. If you trade your 350, I think that you are about to start working/paying on the same education that the current pilot 400 owner is tired of working on and paying tuition on.