Your best option would be to have a string at the start of the dungeon which changes based on Link's counters or which items he possesses. Then the string can give Link a custom item "WarpDummyA" which--when coupled with an appropriate script--triggers Sidewarp A (repeat for B, C, and D).

@bigjoe made a simple FFC script that checks for WarpDummy in Link's inventory and then draws a combo with the "AutoSideWarpA" type (at least I think that's what he did). I'd try to write a similar function for you but I'm a little rusty.