(1) In the past I have used jv16 PowerTools, TuneUp Utilities, and Ace Utilities, and I still believe these are among the best (and safest) registry cleaners. However, I no longer use registry cleaners because the risk is too high. Sooner or later you'll get brave and delete some reg keys which shouldn't be deleted and perhaps introduce instability to your system.
Having said that, as long as you have some "safety net" (ie. imaging software, rollback software, virtualization software, or whatever reliably works for you), tweak away with System Mechanic with the confidence any mistakes will be reversible.
(2) Common sense might indicate MBAM's detection of .txt files is not a concern, but common sense is sometimes completely wrong. I haven't run across this issue with MBAM. Can you identify these text files without breaching your privacy? Perhaps somebody has experienced the same results.
(3) Why no AV? Do you run online scanners?