I'm not in favour of limiting substitutions inbetween sets as it significantly limits the amount of playtime players will get, or rather it prevents team captains for balancing it out. Should your team make full use of the 10 players per roster, only 3 substitutions per map would mean that - given everyone turned up for the match - at least one player is garantueed not to play the first map. Especially now that you have reverted the format of ft3 back to the old bo5 it could mean that players have to wait a minimum of 10 rounds before they get to play.
Also following up on the match rule change, the additional flexibility of swapping players during a set could be a suitable counter-measure to the accumulating gold advantage of one team should they win 3 or 4 rounds back to back and will keep sets interessting until the last round.
My suggestion, in short, allow unlimited substitutions inbetween sets, and on top of that a total of 3 substitutions per map during sets. Obviously for each match respectively. I think this is what your rules initially read like and what most players could get behind.