Hmm. Option 3 sounds best. I suppose you could have tried an option 4, which might be called a cross-schedule cross-round pairing, since round 2 of the 3-day schedule was (presumably) played at the same time as round 1 of the 2-day schedule. For one player in each of those 2 games, the game would be round 1 2-day, and for the other player, round 2 3-day.
Then the two 2-day players could play each other in round 2 of the 2-day schedule.
Trouble is, the cross-schedule cross-round pairings would have to be played at the faster time control used for the 2-day schedule, and the two 3-day players in those pairings might not go for that, because they wanted to play slower, and because they would now have a long wait for their round 3 games.
So if you can’t find two 3-day players willing to do that, you could instead pair the two 2-day players against each other in round 1, and then try cross-section pairings in round 2 – after all, both of these players were eligible for the lower section anyway.
Or, if you can find only one 3-day player willing to play at the faster control, you could have one cross-schedule cross-round pairing, and one cross-section pairing. (Would this work, or am I missing something?) I guess these two pairings would collectively be called a cross-schedule cross-round cross-section pairing.
Whew! The life of the organizer of a multi-schedule, multi-section tournament, especially with some small schedule-sections, can be quite complicated. An innovative approach is a huge plus.
To top it all off, I suspect I might have been one of the players involved in this situation, and option 3 might have been used without my even being told about it. That worked out well, too, as I did get to play all 6 rounds, no byes.
Bill Smythe