Hello.
Your goldfish may have been picking on the pleco (hence the frayed fins). It's possible, but I don't think that the goldfish could have killed your pleco. And I don't think it was the filter either.The methylene blue shouldn't have had any ill effects on the pleco.

As for the gelatinous blob... do you have snails? If so, it could be a snail egg casing. If not, I am not sure what that could be.
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Phishie
Site Coordinator

"An ounce of prevention is worth a pound of cure."