Glad to be of help. I was doing a forum search to see if anybody else out there had an old Shogun as well. Picked mine up about 6 months ago (I guess around the time you picked up yours). It was covered in dust in some guy's garage, but in
mint condition. I had been toying with the idea of getting a road bike, but a few things were holding me back. One was the high price of anything reasonable (about $800 to get above the Sora level) and the other was my hatred for compact frame geometry (I dislike the sloping top-tube on aesthetic grounds, but I'm sure I'd get over it with time). Also, it all seemed a little too "serious" looking for my style. I didn't plan to be racing, just enjoying nice long rides around the Finger Lakes region and commuting in nice weather. Don't get me wrong, I could certainly afford an $800 bike, but it seemed like a lot to spend for a bicycle. I can blame my parents for imparting some sense of practicality to me. I couldn't resist when I saw the old shogun selling for peanuts on craigslist. It just has a retro-coolness to it that says "yes, I like to ride, but I'm not one of those gram-counting techno-bike-weenies".
As for your freewheel, Nashbar sells new 6-speed freewheels for about $20 if your old one is shot. As does Harris Cyclery
http://sheldonbrown.com/harris/freewheels.html#6. Of course, your shifters are non-indexed, so you might want to put a 7-speed on there if you were to replace it. The derailleur will handle it just fine. Just be sure to get a 7-speed chain to match the slightly narrower sprockets. If you go online, you will also be surprised to find a wide selection of 27 x 1.25" tires available (I was surprised anyway). I am using the Nashbar-branded kevlar road tires ($6 each when I bought them on sale). They have held up well to the miles I've put on them. I've only changed one tube so far in about 1000 miles.
Oh, other interesting stuff. If you look at the components on your bike, you'll find that it's 100% made in Japan stuff. The "Via" listed on the hubs are the factory in Japan that they were made in. In other words, it's much higher quality bike than the stuff that came out soon after (when manufacturing shifted over to less expensive places as the Yen heated up). It's not collectable (aka it's not worth anything), because nobody knows the brand, but it's still a great Japanese-made "sport tourer" that should serve you well. If you measure the geometry, you'll notice the long touring type rear triangle. A very comfy geometry for long rides with stable handling. It has eyelets for fenders and racks. Strangely, it only has mounts for a single bottle cage...