Good points Furry, and I guess I see many of these things as normal mechanical skills.
The bolts on the 4 engines (even the 2013) I have all have sufficient fasteners. Not great, but sufficient.
You bust them, strip them or cross thread them is operator error. So torque them and run it for now.
A novice is likely to cause more damage by upgrading the hardware with all the disassembly needed and no torque wrench. We have seen it!
Squished cables do happen, certainly obvious defects need to be addressed.
I've had cylinder defects and rough head surfaces but none have affected operation.
Again, having a novice tear into this has a greater likelihood of damage than what they intend to cure.
All modern bearings come with very little lube on them, often just an oil coating.
Read the instructions and lube as needed, that includes the reduction gears. Normal maintenance, in the manual.
So what can go wrong with your suggestion of replacing the hardware and cables, pulling the head and cylinder for checks, replacing lines and grips, lubing and waterproofing everything? Stripped threads and cracked parts, impossibly wrong length and damaged cables, multiple trips or delays to shops or on-line trying to get new or better parts, damaged parts, wrong alignments, wrong lubricants, too much lubricant, slipping clutches, leaking seals from operator damage, endless delays and frustrations from problems and "imperfection". This often leads to parts lost or kits abandoned (Yay! I get a great deal!)
Install it as instructed and you are running in an afternoon, running and learning.
Furry, you have better than average mechanical skills and experience, and great knowledge and expectations about bicycles in general. You are not the target audience. If you are new to mechanics and to these engines, I stand by my advice to assemble as instructed an resist the urge to modify. With a novice it introduces more problems than solves. I back this advice with 40 years of well educated experience in industry. The first thing we do with unreliable machinery is put it to the "as designed" state, and start solving problems from there. I recommend the same thing with these engines.
This is the beauty of these engines. Put it together as designed, knowing it will work well as designed if you do your mechanics well. Then, work on things one at a time, learning and improving.