OK here goes...

My 120v to 24v transformer went out. I replaced it, no problem only 2 wires in and 2 out. When I move the T-Stat to "fan on" it turns on and blows no problem. When I turn the switch to cool, the fan shuts off and nothing. So I check the wiring and here goes

From T-Stat
Rc and Rh jumped - Red wire goes to R terminal on the handler/furnace. In the middle, it is spliced into a separate black wire that goes to a Saf-T Switch flood/water control thing
G - connects to G terminal and controls the fan (no problem)
W - connetcts o W terminal
C - connect to blue wire which seems to be my common
Y - here's the problem - The Y is spliced into the red wire of the outside unit. But at the handler/furnace, its not connected to anything. Any terminal I try to connect it to, the fan stops working and it seems to disrupt the whole process. When I leave it not connected at the handler, the fan works fine.

From the outide unit -
White wire - splices into my blue T-stat wire and is the common
Red wire - splices into the yellow t-stat wire (see above)

Any thoughts?