The guide mentioned was for novices (I believed), technicals that ought to go over your top would be cam durations, piston ring placements, stroking, big bores etc.
Now since the bike is up and running, there is not much left to worry about. Instead you could look forward to riding it and for this, you could somewhat be thankful of the neighbor. I'm sure the instant the bike started up, there were a number of concerns that must've vanished away. The liner has a 40 to 60% ratio of getting scratched up, but then in some cases, the scratches are again honed by the piston rings. Hence not much to worry about anymore. The smell should be of no concern either.
Air and Oil filter
Lube the chain, accelerator and clutch cables, also the speedometer cable if can.
Fix the flat tires (Most probably they won't be flat and will just need some fresh new air) Don't let the puncture people fool you on this.
Good luck and ride safe.