My $0.02 on the things you're still deciding:
1. Let them stack, but perhaps with some sort of diminishing returns and/or cap. If it's a one time buff, then you don't really have to "sweep" the area, you have to find one champion mob and then you get the buff. Allowing the buffs to stack forces you to actually sweep the whole area looking for rares before going to the boss.
This shouldn't diminish the value of shorter play sessions. Someone can still take 5 minutes and get a buff by killing a champion mob and then going to the boss, it just won't be as strong of a buff as someone who took 30 minutes to sweep the whole area before going to the boss. That seems ideal, in my opinion.
I'm not sure what numbers you are working with internally, but let's use an example: On your way to skeleton king there are 5 champion mobs spawned. The first champion mob you kill gives you 20% increased MF/gold. The second gives you 15% increased MF. The third, fourth, and fifth give you an additional 5% each, for a total of 50% max. This both allows shorter play sessions to be very viable (two mobs gets you 35%), but also gives a significant incentive for longer play sessions to go and kill the last 3 rares.
2. If you utilize the above system, allow the buff to persist through death, but drop a "stack" of the buff off with each death, starting with the strongest buff. For example, if you die on the boss with the 50% buff mentioned above, you come back, but only have 30% (the 20% initial stack drops off). If you don't allow it to persist through death somewhat, then rather than finish the boss run, people will just leave the game after their first death. Allowing partial persistence through death encourages finishing out the boss run, particularly because if someone leaves, they may do another boss run where 1 or 0 champion mobs spawned.
3. As for duration, make it until you leave the game. No reason not to. If someone wants to go and kill every rare in the game, diminishing returns and a cap will make that a fool's errand, but they shouldn't be punished for doing so.
I would love to hear thoughts on these ideas.
Overall, great concept. Can't wait to play with it.
This guy knows what's up, +1