I think it very well could have been a combination of the filter change
and the new additions that caused the ammonia spike. The nitrogen cycle
can be fragile in newly established tanks. The majority of nitrifying
bacteria DO live in the filter media and then secondly in the gravel
and decor and very few are just swimming about the tank. I do a quick
swish of the old filter in the water before making the change to a new
filter bag.

Also, when cycling you established enough bacteria to support the
bioload you had. When your fish died and there was just one molly left
some of that bacteria may have died off leaving only what was needed to
sustain the bioload. Adding new fish to that could cause a hiccup in
the cycle allowing you to see small amounts of ammonia. To simplify,
all of a sudden you had more ammonia then your bacteria could consume.

I went through a lot of stress myself when I first learned about tank
cycling and put it into action. All I can say is, once it all works
itself out, it is SO worth it!

Hang in there.