I'm surprised by all this. For a start, I keep mollies and guppies together in a tank and they get on just fine.
Secondly, 6 guppies in a tank sounds somewhat over-crowded, although I appreciate you are diligent about water changes. Still, an over-stocked tank and poor water quality tend to go together, particularly if the tank is not cycled.
My suspicion is that that tank is not cycled and the male guppy caught that guppy tailrot disease that wipes out guppies in a matter of hours (I've lost guppies through it myself). Poor water quality is the most common reason for contracting such infections.
Although you put matured tank water in the new 5.5 gal tank, the vast majorityof the beneficial bacteria you need for cycling are in the gravel and filter. Since you haven't got a filter on that tank, and the gravel is new, I'd be almost certain you've got an ammonia and/or nitrite spike in that tank. Do check your water and confirm if my suspicions are correct.
In the meantime, can you get some gravel and filter media from your established tank and put it in the 5.5 gal? Also, put some salt in there - it will help keep tailrot at bay and help the females cope with the stress a little.