In my experience, the way to build a nice running, inexpensive, reliable 400EX is to do the following (we've built several of these):
Ross 87mm piston (the only piston assembly that doesn't outweigh stock)
39mm FCR carb
Mild head work - mostly port matching & a little bowl work
HRC cam (or a Web 450/451 if you want a little more top end at the expense of bottom - Hot Cam S2 if you don't want to spend the $$$ for the HRC)
Open the airbox a little (do not remove the lid - drill a vent behind the filter & install a port)
Pipe of your choice
8 plate clutch setup of your choice.
These mods will make it accelerate as fast as a stock 450R (power will be delivered much differenly though) & as reliable as stock.
The quad starts more easily than stock, runs well, and doesn't require any additional maintenance.
This is the same setup we ran at the 12hrs of America last year - won our class and came in 14th or 15th overall against a field of numerous YFZs, 250Rs, etc.
There are a few other tricks you can do to bump power up a little more without getting too wild, but those detailed above are the basics.
This will not be the fastest 400EX out there, but it will be much faster than a typical 400EX or 440, very reliable, and won't break the bank.