According to your info, a game could take up to 4 hours, WITHOUT the increments. Increments of that magnitude just INCREASE the time control. I can make a move every 30 seconds and the time will never decrease.
The 50 move rule shouldn't exist!

My answer depends on the situation. If it's one game per day, then just say it has to end by a certain time, like 5pm, or something.
OMG, just make it 100 already. Who cares if it's exact.
I think it would still need to be different for different numbers of men. Probably 49½ would do for all 5 man endings, but if you made it 99½ for 6 and 7 man endings you'ld still have unfair terminations of winning play. It would always be possible, with perfect play, to win any won endgame, but the lower you make the move limit the more accuracy you may be forcing on the players.
A typical situation would be in KNNKP. If as, White, you miss a mate in 18, you can finish up having to play the full monte. If your opponent claimed under the rule at the point you missed your mate, then with a 39½ move period you could well find yourself more than 18 moves away from mate at his next claim even if missing the mate were the only b*llock you dropped in the whole endgame. Changing the number of moves to 49½ would probably fix this for KNNKP, but not if you dropped a similar one later.
In fact, in the second case, the player need not be playing 49½ times sub-optimally as I said earlier. It could be only 4 or 5 times sub-optimal. The problem is that he isn't dropping his moves evenly across his whole endgame.
I would expect this problem to need even more moves to fix for endgames with more men, but I can't play any pawnless endgames with more than 5 men with any sort of accuracy, so I'm stuck to say what the numbers should be in these endgames. You can't get the answers from EGTBs.
Certainly zeroing the move count on irreversible moves would go some way to fixing the problem because a claim for a particular endgame could only first occur n moves into the endgame. This would fix KNNKP even with a 39½ move rule.
I'm about to send FIDE an e-mail. What should I change?
1. FIDE have already eliminated the 50 move rule as a basic rule of chess. It's now only retained for competitions.
2. I think EndgameStudy has eventually abandoned his time limit ideas.
I'm about to send FIDE an e-mail. What should I change?
1. FIDE have already eliminated the 50 move rule as a basic rule of chess. It's now only retained for competitions.
2. I think EndgameStudy has eventually abandoned his time limit ideas.
Belay that. I was writing as you were posting. I see EndgameStudy has not in fact abandoned his time limit ideas.
In fact I've just notice that ES has confirmed that.
Don't worry, I'm about to send FIDE an e-mail so they'll resolve this. Hopefully they agree with EndgameStudy!
FIDE don't have a very good track record with this rule (see e.g. #489). They have just removed the 50 move rule fom the basic rules of chess without any replacement, so the casual player now has no way of terminating a pointless game against a stubborn opponent who will not agree a draw (e.g. Rybka) other than resigning.
The repetition rule will not help, because they've removed that as well. Don't bother trying perpetual check any more.
How could they remove perpetual check? That IS a draw, theoretically! That's a solid draw
Not any more it aint. If your opponent refuses to agree a draw you have to either find something different or resign.
(If it's a tournament arranged under FIDE rules you're still OK because the rules are retained in the COMPETITION RULES section of the handbook.)
Then one of you eventually dies. But the withdrawal rules apply only to tournaments, so I think in that case the result is undefined.
There's still time control on the clocks. The time limit would have been in addition to the time CONTROL