Too bad I sold off all my RD350 road race parts. You might've found things like the CalFab swingarm useful.
The RD250 will work fine. Find yourself a set of RD350 pipes, and I think they bolt right on. I forget the 250 carb size, but the stock 350 carbs were 28mm. Running 32mm on a 350 really woke it up with some mild porting. Any of the road race porting should work well for you and is easy to do.
What do you want, torque or hp? If you want hp, go with bigger carbs. If you want torque, stick to 28-30mm.
You may need to slice/dice the expansion chambers to both exit on the right side or you'll be dragging the left silencer.
The RD400 swingarm is longer if you want that. 250/350 wheels will work on it, but you'll need to make a spacer for the right side to hold the axle.
Get a magneto system so you can ditch the batter. I hate PVLs, and would not recommend them. Their timing curve is all wrong, and they're expensive.
There's an expansion chamber company in texas that makes flat track pipes... forget their name. Not Jemco.. there's another one.
"There isn't any secret," he said. "It's all very obvious."