Have not looked under the fork boots yet, but I will tomorrow. New Hyperpro progressive rate springs, old oil shiponed and replaced with dex/merc after flushing at 131 miles. Filled (by volume)to the low end of the spec in the manual. Consistantly hearing loud clunking sound from fork legs over larger bumps. Shocks seem to beworking fine. I am certain that all parts were installed correctly. I only put about two miles on the bike prior to the new springs, so I have no reference in terms of shock noise.
Dusty
Since this is the internet and we can't hear the "clunk" here are a few possibilties.
First of all you should ignore the volume measurement and use the actual oil height, set with the springs removed and the forks compressed. You should also manually cycle the forks few times before you install the springs and caps and check the oil height again. If you didn't do this and you've only ridden a couple of miles your forks could be cavitating (air instead of fluid in the space between the fork tube and the fork leg).
Typically aftermarket springs are longer than stock. If no spacers were provided and you've used the stock TW spacers you could be in coil bind. Also, if they aren't perfectly centered in the fork tube or if you put the upper washer upside down they could be banging the inside of the fork tubes. You may want to seek some advice on spacer length from someone who's using them. I think there are a couple of posters running the Hyperpro springs.
Could also be your upper triple is loose above the top bearing, or that the steering bearings themselves are loose.
Another really remote possibilty is that (if the springs are progressive) there are far fewer coils on one end than the other. These coils would take up less oil volume than the tighter windings, leaving an excessive air gap. If it were my bike I'd put the tighter (closer together) coils in the oil (down) so that the oil level would be closer to correct once the springs are installed.
The other really ugly possibilty is that the bore of your lower legs is worn out. This will require complete disassembly to check, so look into the other causes first. ATF is cheap. Start with the oil level, steering bearings and check the upper tree.