I am going to guess that the micro bubbles are coming from your Remora C skimmer. Did the skimmer come with the overflow box for inside your tank? If not you could purchase one as the return side of the overflow box has a foam pad on the bottom of the outlet side to prevent micro bubbles from going into your tank. Another option would be to put a piece of foam on the right hand side of the skimmer just behind the waterfall outlet. This will trap microbubbles before they have a chance to enter your tank.
The FX5 is a large canister filter for a 54 gallon tank as it is rated for tanks up to 400 gallon. It may be over filtering your tank but some members will say there is no such thing as over filtering. I have a 90 gallon tank and only run the Fluval 405 canister filter as it is rated for up to 100 gallon. If you want to try a smaller filter let me know as I could swap you my 405 for your FX5 for a while if you want to see if it makes a difference.
Good luck with your tank and keep us posted on your findings.
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