Depending on what you're doing, finding exact top dead center requires a degree wheel and a piston stop. There's too much range the piston stops for to accurately get TDC. If it's for the timing chain, look for the T mark on the fly wheel. The F mark is for checking ignition timing (aka Fire). The T mark is accurate enough for the timing chain, but can be unreliable for ignition timing when modifying (sometimes it's stamped off a little from what I've read).
You can pull the engine out as a whole unit, but taking that extra stuff off would probably make it easier. Might have to pull the starter to get more room to work and maybe airbox/carb. I don't work on the 200 series engines a whole lot so can't remember how I pulled
parts machines apart lol.
Since there isn't a whole lot of room to work around the spark plug hole, you might be better off pulling the engine out of the frame to try to fish it out, then you can use gravity to move it around and some long narrow pliers or tweezers to try to fish it out.
If you do take it apart, I'd say new head gasket, maybe new base gasket for the cylinder if it breaks loose or has any signs of leaking. For the top end, since you'll have it off, I'd inspect the head, make sure the valves are seating well. If you're up to it and have the tools, replace the valve stem seals. Re-assemble the valve cover with permatex GRAY RTV. It gives you a lot more time to work with to assemble, but takes 24hr to cure. Hondabond, Yamabond etc might setup up really fast and if it sets up too fast it won't seal. I don't remember the name of the stuff, but there's a bunch of people that swear by another brand that's like Hondabond in the porting/build chainsaw communities, but it sets up in something like 30 seconds. Also, if you care about the decompression system on the 350x, make sure everything is loooking good in that area, no excess wear etc. A new seal for the shaft isn't a bad idea. If it doesn't work right you might need a new cable, not sure if it can be adjusted. Some people just pull the cable and live with out the decompression system, but you have to learn the trick to starting it, and you get worn out quicker if you can't get it to fire up right away. No decompression system puts more stress on the kick starter system, but I don't think this machine has any real issues in that area so shouldn't be a problem.