The best thing you can do is get a factory shop manual for your engine + drive package and read, read, read. See the problem is this: if you're younger than about 55 or so, this is stone age technology to all the younger folks who grew up with modern, electronically controlled engines. I'm in the AARP range now (LOL) but I grew up with simple engines, that had points and condenser ignitions and carbs. So to learn how to maintain anything you had to learn this stuff.
The technology in boats of this vintage, is very similar to GM automotive tech circa 1965-1975 or so. Just before electronic ignitions and cat converters came on the scene. Why, because the EPA did not stick their muddling fingers into it, yet. Now you have the magic of I/Os with cat converter exhaust, EFI and electronic ignition. I have no problem with electronic ignition, but if you buy older boats you probably will have an easier time with a carb vs EFI (because, for EFI the parts cost more and when the boat gets old, they get discontinued and you are S.O.L.). Cat converter exhaust I would not want under any circumstances. $3000 a side to replace. No thanks EPA.
Back to your questions:
yes the nut on the top of the flame arrestor should be all the way down. That flame arrestor (instead of an air cleaner) is there for safety, if the engine ever back fires through the carb, it will prevent a fire in the engine compartment. Any mechanic who would give you the boat back like that is incompetent!!!
The hoses are supposed to go to a rubber grommet in each valve cover and run up to the outside mesh of the flame arrestor. This is to allow blow-by gases from the crankcase to be sucked into the carb. No PVC valve like cars have but some newer engines may have them. The screw you labeled is the idle speed screw.
Read, Read, Read, Learn all about marine Quadrajets because that's what you got.
Find a better mechanic.
blurry pic of mine but you see it here:
https://www.dropbox.com/s/rnbgbvteib1b0 ... t.jpg?dl=0