Nope. It's never a bad idea to flush your brake fluid. But it isn't mileage that matters, only time. So if that 5000 miles was 2 years, you were right on schedule.
I believe that it is the rubber hoses and seals that stain the clutch fluid. The clutch seals are much different than brake seals. They are designed for a much lower pressure. The big difference is that each time that you operate the clutch you are pushing a much larger volume of fluid up and down the lines to drive the slave cylinder out far enough to disengage the clutch. In the brake system the pads are very near the rotors already, so there isn't nearly as much fluid movement through those lines. It is perfectly normal to see the clutch fluid stained that way, and acts as a nice reminder to flush all of the fluids again (the brake fluid doesn't change appearance much)
As you infered, regular flushing of the brakes doesn't get all of the fluid out of the ABS pump. To do that you'll want to flush the lines (as you already did), then operate the pump using the test jumper and test procedure, then flush the lines again. It's a good idea to do the test at every flush anyway. Even if you don't flush the lines a second time, any small amount of old fluid released will be diluted by the new stuff. Plus you will confirm that your ABS is actually functioning correctly.
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