1....why not just re serve to get the right fit? if its just slightly tight and a new serving it will usually wear in some. Ie if you start filing/sanding/whatever new nocks on a new serving, they'll likely end up too loose down the road rather quick depending on how much you shoot.
Serving is easier and more consistent than trying to tweak a nock either sanding boiling or any other method. even if you cant make a string, serving is a cake walk and something that is a good skill to have. I sat in a bear stand this spring trying to fix a serving that had gotten nicked and started to come unwound. If you cant serve, that could have been the end of a hunt

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2. if its wood, look at the grain to make sure its orientated right. if its aluminum/carbon it doesnt matter as much as long as you dont have a fletch contact problem. some shoot cock feather in. I dont, I prefer cock feather out my lower hen feather rides in a grove between the side plate and the shelf material. Keeps wear down...atleast thats what I tell myself.

Down would lead to bounce problems I would think. You could fix it somewhat with a high nocking point if needed....tuning will tell you what to do here.
3. I assume you mean the rubber kids looking thing. I know a guy who uses it and likes it, but I dont know how long they last. He also likes to shoot bare fingered. I am a tab guy who recently went back to glove shooting. Best thing you can do is give it a go and see what you think of it.
Lastly improper nock fit will affect arrow flight. Giving you inconsistent flight if its loose and a possible dry fire (been there done that). It leads to problems like knock pinching, trying to hold the arrow on the string..... Too tight will give you a over stiff 'reading' when you are tuning (its a dynamic spine game, kind of like changing point weight, the arrow stays on the string longer and in doing so you'll also loose some performance). They can also break nocks in the cold (been there too LOL). Try hunting hares at -40 with super stiff snap on nocks...yay! If I error I prefer to error a little snug than a little loose. But not tight. Again the serving will usually wear in or compress...so a skosh snug (again not tight) will usually be perfect when that serving is worn in. If it gets a bit too loose you can always cross hatch with dental floss and tie off creating a second lower nock with the df. the cross hatching amount will depend on how loose the nock is on the string.