You shouldn't because it's not really the right way... Plus, you'll never get ALL the crud out of your forks if you don't take the top bolt out.
Unfortunately, it's a discontinued part, but I'm sure you can take the one you have out to a motorcycle shop or a machine shop and they'll be able to tell you the specs on it... that way you can potentially find a fork cap from another bike that will fit yours.
I'm 99.99% sure they're a 38mm fork... so...
http://billetparts.co.uk/catalog/produc ... ucts_id=58I don't know what the pitch and size of the stock thread is... so that's something you need to find out.
Other than that... you need to remove the caps and empty out the forks of the springs, damper rod, etc... and let them hang upside-down for about 12 hours to FULLY get all the gunk out. Then you can worry about a refill.
You don't "NEED" vented caps on that bike either. I suppose it's good for on-the-fly adjustment, but they're not a pressurized shock... they are simply a neutrally-buoyant system, so it's not a necessity.
For removing the other leg's bolt, you've got to re-install them in the triple clams, get a good sized pipe-wrench and stiffly give it a jarring to try and break it loose. Might help to have a buddy hold the bike. Otherwise, bench-vise... pipe wrench.
You may have to elevate the situation to vise-grips and a hammer... but that all depends on how goosed the PO made it for you.