Northocean, if the boat was built 5 years ago, it will most likely have a glassed deck if the builder followed the kit/instructions. It's not really that big of a deal unless you're doing a lot of T rescues and the like. The glass definitely gives the boat a lot more strength, but people paddled boats with no glass on the deck for many years before going to the glassed decks. As I said, the biggest noticeable reason for glassed decks comes in when doing assisted rescues. Not a lot of people do those types of rescues and if you don't envision yourself doing them a lot, don't worry about it too much.
You didn't mention your weight, but it's likely that the boat is a standard 17 (vice the LT) if it felt really big on you. The LT typically feels more like the "tight" fit you describe. As example, I'm 6'1 and about 165-170 pounds and the LT felt much more "comfortably tight" on me. I ended up buying a smaller beam boat, but the 17 felt substantially larger, to me, than the 17 LT. The WR18 was just gigantic.
As far as the hatches are concerned, those are the standard CLC hatches and they keep the water out well, assuming they were built correctly. There are improvements that can be made, but likely you won't need to worry about them.
The foot pedals can be moved if they don't fit you very well. It's not a really difficult process to unscrew them and relocate the rails a few inches. You may need to add a little adapter plate if the rails are mounted through the hull (so you don't have to drill new holes through the hull) but other than that it's not much work at all to move foot pedals around.
Fishbuster is right, you can pretty much completely redesign the fit of the boat with very little effort and expense. A bit of foam padding here and there can drastically change how a boat feels to the paddler.
I'd say the big concerns you should have are any patches, weak spots, and obvious damage. Go over the whole boat carefully and feel for any weak spots and flexible areas (more flexible than the wood around the area, not just flexible as a whole) and any obvious repairs. Ask the owner what kind of repairs and maintenance have been done to the boat. Was it stored inside or out? Is the deck glassed or just epoxied and varnished? Look for any black spots on the wood surfaces that aren't painted. (Black spots indicate water damage to the wood.) For the rudder, check for any cable fraying, and make sure it rotates (up and down as well as sideways) easily without any hesitation or "tight" spots. Check thoroughly around the coaming riser and verify the integrity of the coaming against the deck. (Mine separated from my deck from me sitting behind the cockpit while entering and exiting my boat--but that was due to a design mod I made in mine so shouldn't be an issue for a Chessy.) Look at the bulkheads inside and verify the integrity of the seams against the hull and deck.
My last bit of advice would be to get an opportunity to actually paddle it in water before you buy it. See if the owner will meet you at a local paddling area and let you take it for a spin. If not, if it's in good shape and you think it's the boat for you, buy it anyway. It's less than you can buy the kit for now and you'll be able to paddle it immediately.
FrankP