SaltH20cowboy, If the membrane are the problem, then they must be clogged from the inside out.
We tried CLR over the years and found that it cleaned only for a short period of time. We worked with a supplier manufacturing a new natural product that is not hard on the water but that cleans very well mineral deposits in water pipes.
We used it on our Bubble tubing and our diffusers and found it to be the best product we have ever worked with. It is not harsh on the water; fish or membranes won't make a hole in you hands or pants... and remains clean for a long time. Its called bio-purge, it's on our website:
http://www.canadianpond.ca/biopurge.html Simply put, you unplug your airline, take a funnel and pour a liter for each 2 disks and 200' of air line. Plug the compressor back on, run it for one or two minutes, stop it and wait about 30 minutes. Then let it run again to flush it out and see the results…
Only draw back is that this stuff looses its potency after 6 months. So you can only buy it for an application when needed, and then buy fresh stock when needed.
This is our solution for cleaning membrane, disks or tubing... Of course as Ted said, I would look into all the other items first as the problem might not be related to a plugged membrane.
A litre sells for 20$ and a 4 litre jug for 75$.
Good luck!