I have a vacation home in upstate NY that has a Thatcher oil
furnace.Recently it had a problem with firing up. It turned out that
there was an air pocket in the line after a new oil line was run to
the tank. I was not sure how to bleed it. There was a flathead screw
on the motor assembly that I opened, and I did see a little air come
out, but it did not help. Then I opened one of 2 hex type bolts on the
top of the motor assembly, and that cleared the air pocket.
I'm trying to familiarize myself with how the system works, so here
are a few questions.

1) What are thses hex bolts for? Are they for bleeding or do they
control oil flow?
2) Do the burners need adjusting, and how are they adjusted?
3) There is a Honeywell stack switch at the base of the flue pipe has
been disconnected ( wires were cut) what was the purpose of this?
4) I have a Honeywell fan limit switch L498 that has an off-on-off,
that has a high limit of 200 deg which is suppose to shut the system
down if it gets too hot. Does this take place of the stack switch?

Thanks