ulceration (fish TB? other bacterial attacks) can be a result of funky water, which evidently can set back the immune system. They take time to develop.
I would be careful to keep your water quality as good as you can. Many bacteria, including the Mycobacterium which can cause fish TB, are commonly found in aquariums. They are benign unless the tank gets too dirty.
I was really surprised to hear Terry Fairfield suggest that "bacteria are really pretty wimpy parasites." :) What he was saying is that our aquarium fish are usually pretty able to resist bacterial attacks. When we let the water get a little iffy (hence your cloudiness) then the fish's immunity isn't so strong and the bacteria can get into their systems.
I'm guessing that the Start Enzyme didn't hurt the fish. Additionally, it is obvious that you were concerned that the bacterial level and pollution were a bit high. I think that your water changes, followed by the addition of beneficial bacteria via the addition of Start Enzyme is a pretty resourceful approach. You may well have benefited your remaining guppies.
Watch that your guppies are eating all that you give them. You have a modest number of fish; it is easy to overfeed them.
Another seasonal challenge is the wildly fluctuating fall weather. Our Chicago area temperatures have really varied lately. Night time lows have been in the 40s F and Chicago recorded a record low 39 F/ 4C a few nights ago. We closed the windows, switched on the furnace and the house's circulation fan to keep tank temperatures from fluctuating too dramatically.
I am concerned for some new guppies (young golden bodied, red deltas from a wonderful strain) who followed me home Saturday. One doesn't need their temperature jerked around.
Still in jars as their rather different water is adjusted, I took a page out of your book. I added a drop each to the jars of Ultimate (perhaps the best new water conditioner, maybe the best for fresh water fish) in order to chemically lock any ammonia released by the fish. They will be ensconced in their 10-gallon tomorrow.
All the best!