1) The vacuum lines:
Yes, you can cap/pull them out/set fire to them..whatever.
The computer received inputs from various sensors and then used the vacuum lines for various fucntions. With the ECU not in the loop anymore, the lines are not serving any function.
1a) The idle tubes: To get them completely clean, you will have to at least remove the air cleaner holddown, the choke plate, and the choke linkage. I can do this in about 3 minutes. I'll post some pictures later to show you what I'm talking about.
2) Essentially the "idle jets" are the mixture screws on the front and the reason the "directions" tell you do do it while it's running is so that you can tell when the RPMs drop. Ones the RPM's drop, you're supposed to turn the screws back out (enrichen the mixture).
I have access to a narrowband exhaust gas sensor, and I set mine with that then set the idle like you normally would with a fully functioning engine.
3) You will want to remove the vacuum line from the vacuum advance port on the distributor when you're setting the timing. You don't have to remove the 4" and 10" lines from the firewall, but I usually do it anyway.
Then you can set the timing to spec.
I would recommend setting the timing first, then doing the idle because the timing will affect the idle.
If the timing is at something like 12* it will idle higher than if the timing were at say...6*.
EDIT: Here are the pictures...
This one shows the carb and components that need to be removed to get the venturi cluster/idle pickup tubes out.
Red: Are you will be working in.
Green: Air cleaner holddown.
Blue: Choke linkage.
Pink: Choke plate (vertical in the picture).
Light Blue: Two venturi cluster screws you'll need to remove.
And the same picture without any colors on it so you can see what everything looks like.
This image shows the venturi cluster removed.
This one is the idle pickup tubes removed from the venturi cluster.