At face value the issues were not show stopper and like you, I was not too concerned about the leaks and assumed tightening the bolts or disassembly, clean and reassemble would fix the issues.
Re the Flywheel, that was an easy fix, I spun the fly wheel in a drill chuck and used some 400 grade wet and dry paper to remove a couple of thousands of an inch, and now the fly wheel no longer makes contact.
For the exhaust flange, when the bolts were tightened and the engine running, it made no difference, it still leaked. I disassembled the exhaust flange and found that when the pipe was manufactured, the flange was not fully formed and flat, so even with a gasket, it would not seal.
For the valve chest cover, my attempt to tighten the bolt revealed that the bolt just spun round in the hole, there was no thread for the bolt.
I contacted the seller in China, they responded the same day asking to see videos of the issues, which I sent them. The next day they offered to send replacement parts and sent a video showing how to dismantle the engine. I went ahead and disassembled the engine to confirm the parts needed, as I did so, I also found another stripped or missing thread, this time it was one of the bolts holding the cylinder head on. Here are the photos, note the stainless steel insert cylinder liner, and the quality of the machining.