Many teams publish basic numbers. You have put quite a bit of thought into this already. Obviously there are some unknowns that have you concerned. Visiting the team sites would address many. Like cog belt drive being very common for cams. Teams post the data because they know making everything come together is much harder than having the data. One of the engines I've seen had a very large "something" on the crankcase. I can only guess it had something to do with crankcase ventilation, but it was huge.
Your understanding of how CNC is used is very basic. I certainly doubt you can run one or even a few cylinder liners and expect the sort of tolerance you think you'll achieve. If you are very familiar with the machine, the tooling, the material, etc., you might get a part that's pretty close. The kind of tolerances you're talking about require an expert operator to achieve. My father runs setup and production on CNC lathes, using softer material and much smaller parts, and has to chase the machine to get a 25 micron tolerance. One comment, you won't be honing the liner until it's installed in the block unless you can be assured the block is as round as you want the finished cylinder to be or the liner is stout enough that it won't distort.
Nemett has a tube connected to the head. Fluctuation of crankcase pressure forces some oil to the top. You could get creative and check valves in a few locations to assist the flow. Most of the Eco engines seem to have open top ends. For the short time they run, lubrication can be handled a variety of ways. On vibration, I think most is due to single cylinder torque.
You really should just get on with a design. You'll find, much as I did, making everything fit to meet design goals will be the hard part. These engines run ridiculous compression ratios. Valve timing, valve clearance, valve lift, valve angles, piston and combustion chamber shape, etc., will all interact in the final outcome of the design.
Cost, won't be out of line. If you have access to machines that can handle the sizes of parts involved, costs will be mainly tooling and fixtures. Grinding cams could be tricky. If you plan on using something other than a simple cast iron ring, a stock ring for a production engine can be very inexpensive, or a custom faced ring might be hundreds if not thousands. Checking to see what parts are available and basing the bore around that might be well worth the investment in time. Similar to the wrist pin bearing. Most <35CC engines use an 8mm wrist pin and corresponding needle bearing, maybe 6USD for both. Stray from that and you'll at least have to make a wrist pin, harden, grind, etc.
It's a great project to be involved in. Sometimes I think about going to college to get in on one of these. Good luck.
Greg