I'm not an engineer or conductor myself, but I've been a safety consultant for the railroads for 13 years, I do work for 2/3 of the US's ~600 railroads, and I've personally been to about 80 of them, so I can help some.
First, on something you didn't ask...the vast majority of railroads in the US are small, short line (Class III) or regional (Class II.) About 80% of the railroads in the US have fewer than 25 total employees. Most of these don't perform road service (long distance travel from point a to point b and back) but rather yard switching (building the trains and putting cars where they need to be) and local/industry switching (taking loaded cars to customers and putting them where they need to go and then taking the empty ones away.)
The FRA (Federal Railroad Administration) requires locomotives to have 'sanitation compartments' with toilets, but there are a ton of exceptions, and of all of the railroads I've visited and the locomotives I've been on, very few locomotives built before 1980 (so, most of them) have them. Here's FRA's rule on it: https://www.law.cornell.edu/cfr/text/49/229.137 - since I'm dealing with short lines a lot, typically they're in a yard so they can just stop and go inside and use the yard office bathroom, or they have agreements with specific customers to use their facilities during switching. Some others put portapotties along the tracks. For the rest, rural trains which aren't near anything resembling society and on old ass 1970s equipment with no toilet, they stop, get off the locomotive, and go in the woods.
This applies more to Class I railroads, very few short lines do this type of work. Employees are federally capped at 12-hour shifts. Most short line employees work 8-10 hours per day. So they'll report to the yard, get their paperwork, and go do their job for the day. Even the crews which work full 12-hour days are typically back at the same place at the end of the day.
This really goes to my answer to #2.
Varies by railroad and by crew a lot. I've been on trains which are 2 miles long, but most short lines are hauling 10-30 cars. Some will just take one car out if they're a very small railroad which only serves one customer.
Depends on the job. For most short lines, the locomotive is parked in the same spot it started. For other, bigger ones, they'll switch customers all day and when it's time to stop, another crew comes and takes over the locomotive. Or, the locomotive is stopped on a safe side track somewhere and locked up.
Doesn't apply to most railroads. The few bigger Class II railroads which do Point A to Point B work will either put employees up in hotels, or they have yard bunk houses which the crew will sleep in.
Varies by railroad. Some short lines, the employees just stop and go in the yard office and eat in a normal break room. Others, the crew never stops, they just pick out of a lunch box they brought with them all day. Others, they can stop the locomotive somewhere, get off, and go in a gas station or restaurant to eat.