1. Should be able to. Can't see a reason why not. Do Comair (I presume they operate HRE-JNB) offer Online Check-in?
2. Yes if it is on the same booking.
3. Pass
4. Depends on what you mean by major schlep. You go through passport control, then through the baggage hall. Up an elevator and back to the other end of the terminal. Probably take about 5 mins after going through passport control.
If I had a four hour layover at T1 I'd go to Arrivals Lounge to get a good breakfast, have a decent shower and massage, then go through to the domestic lounge.
5. Yes as you are on a connecting flight you'll be allowed in on basis of your longhaul F boarding pass stub.