Two things to consider...
1. Air gap/fork oil level. The level of the fork oil in the tubes controls the air gap above it, which operates as a partial air spring. Higher fork oil level (less air gap) increases the effective spring rate near the end of the stroke. Conversley, lower oil level decreases the effective spring rate near full bottoming. As Jay mentioned, if your forks feel harsh, you may have too high a fork oil level.
When I installed the new "Progressive Suspension" springs in my 600, they recommend much LESS oil than stock. This is because the spring is longer, with a much shorter, if any, preload spacer than stock. This effectively raises the fork oil level as the suspension compresses much more that stock, causing the forks to get harsh or even hydraulic lock, near the end of the stroke. Check the instructions that came with your new springs and ensure that you have the correct amount of fluid in the forks.
2. Preload - Again, on my 600, "Progressive Suspension" recommended that the springs be flush with the top of the tubes when installed, resulting in approx 1/2" of preload as you screw in the caps. I found this too little preload for my weight, luggage and riding style, and I have gradually added approx another 1" or so of preload to get the forks feeling right to me.
On the 400, with your own variables, you results will likely differ.
Once you ensure that your oil level is approx correct, you can do a couple of tests to help set preload. Put a "zip-tie" around one of your fork legs to serve as a stoke gauge. Lift ALL the weight off the front forks, and push the zip tie down, let the bike settle on it's own weight, then raise the bike again and measure the amount the forks compress with only the weight of the bike. This measurement is call "Unladen sag".
Do the whole proceedure again, but this time sit on the bike in your normal riding position, feet on the pegs. This is called "Laden sag".
Also, do a ride around your normal circuit, and see how much the forks move. As well as hiting some good bumps.
At this point you have a few measurements that will help you. As a guideline/starting point you should have approx:
Unladen Sag - 10-15% of total fork travel. So about 1/2 to 3/4"
Laden Sag - 25 - 35% of total fork travel. So about 1-1/4 to 1-3/4"
Normal riding with NO serious bumps - about 2/3 travel or about 3 to 3-1/2"
Bumps should allow the fork to stroke fully, so about 4-1/4 to 4-1/2"
You want the forks to stoke completey on bumps. If they don't, you can lower the oil level. If they bottom too much, you can raise the oil level. More preload will decrease sag. Too much sag will cause the forks to use up too much of their travel too soon, dive excessively on braking and usually cause the bike to run wide on corner exits, as the bike dives too much on the way in, then rebounds too far on the way out.
Just some suggestions to try...
Also, check out this thread:
http://forums.banditalley.net/index.php?topic=10853.msg87057#msg87057