Hey, I've got one of those 400 WR's as well.
I adapted a set of forks from a '96 Husaberg I have. Great setup. Love the disk brake! It was my uncle's bike and only has 1300 miles on it. Had the side cover corrosion issue and a large hole in the piston. I put an aluminum side cover on it and installed a new piston. It runs really well for having sat in my uncle's back yard for 25 years. It had a 15 tooth c/s sprocket on it which worked well in the desert but I spent way too much time in first gear on single track so I switched to a 13 tooth. That transformed the bike and tightened up the gearing nicely. If I were to MX the bike this is the gearing I would use. Not sure what the tooth count is on the rear sprocket but, since it still had the original Trelleborg tires that it came with, I suspect that the rear sprocket is the original.
The engine doesn't hit like a 500 so, to keep up with them, you'll need to rev it...which you should have no problems with if you're used to those 250's. I recall the days when I had an '84 250 CR and you really didn't get anywhere when trying to lug the engine. The 400 is definitely not like that. I'd say that the top end is only slightly stronger than the 250 but where the 400 really makes up the difference is in the low end and mid range. The vibration in my 400 is not enough for me to take notice so I'd call it a very smooth running engine. The transmission shifts very nicely although I've hit a couple of false neutrals recently. Granted, I cold have been a tad more deliberate with those particular shifts. You're on the right track with those heavier springs as I suspect that the shocks were sprung for a 150 lb rider originally. I'm 245 lbs in my riding gear and it's bottomed really hard quite a few times. I'm currently considering my options for the rear shocks.
Good luck with the project...and have fun!