Oh, man! Jen... I'm so sorry! *hugs* I know exactly how difficult it is when something is wrong, and you can't figure out what. . . or how to help. New filter, loaches are really sensitive to any changes, cycle-wise. Did you use all of your OLD media in the new filter to seed it? Possible mini-cycle due to the filter switch? Water testing clean?
I don't have a Fluval canister, it sounds like the filter basket intake is much better designed than the Eheim that I have (which my loaches seem to enjoy crawling into). The 'like' was for your new filter. . . not the rest of that post. Gah, I'm so sad for you! As far as the filter flow is concerned, I had a difficult time figuring out a way to get mine to be good for my tank's inhabitants, too. One trick I found was to spin the spraybar around so that it's facing the tank wall. This will force the incoming water to 'bounce' off the tank wall, and then go off into the tank - effectively slowing the flow. You can also drill extra holes into the spraybar - even in different directions, if you wish - more holes = less pressure. Many people also will buy PVC piping in the proper size from the home improvement stores, and custom make their own filter outputs. It may take some ferkling with to get this figured out, and it could very well be that the change in the flow of the tank could be stressing the loaches - they prefer calm waters, from what I understand.
Doing a few extra water changes can't harm anything, if there is some toxin in the water - and can even help in the case of some illnesses. In most cases fishes kept in pristine tanks will be able to heal themselves, so bumping up to 2x weekly water changes for a bit won't hurt anything, and possibly help.
I wish I had some more concrete advice to offer you, DON'T stop watching your tank, even if it makes you sad! It's really important to give everyone a good look-over several times a day, in the hopes of fixing on something that may be 'off' in their behavior, breathing, coloration. . . ANYTHING to give a clue. HOPEFULLY these deaths are completely unrelated, and everything settles down now. . .or that someone on the illness board with more experience has been able to give you some idea into what may be going on. Chin up, kiddo! It'll settle down, or you'll get it figured out - just hang in there, and don't lose hope on your beautiful tank!
I'm sorry I've been away, stomach bug has got me down for a few days. . .