6061

I'd like more info about your process before I get too technical, but I will assume that you are doing Type II decorative anodizing with no dye. 

6061 is a high-Mg and high-Si alloy, with a good amount of Cu and Zn thrown in.  The key to getting a good anodize out of this alloy is pretreatent.    As long as you are supplying the "normal" 12 ASF (amps per square foot) of current density at the "normal" temperature of 72F, you should be able to anodize for 15-45 minutes and get a good coating.  A 24-25V rectifier should be sufficient. 

The pretreatment  and posttreatment of the process are the real keys to your success.  A good quality degreaser is required for any machined pieces, and if the parts are dirty.  An etch may or may not be required, but I generally recommend it for the best performance and fewest problems.  The De-ox/de-smut step is often considerd the most important stage of pretreatment.  Ideally, a chromated de-ox would be best, but many locations cannot us chrome (or at least they are penalized for using it).  ROHS-compliant shops should not use a chromated de-ox, obviously. 

For the post-treatment, a good high-temp seal is important.  I've seen some mid-temp nickel acetate seals work okay, but the high-temp seals are SO much easier to use and forgiving of a bad anodize job.  There are other seals available, but the nickel acetate has become so popular, I can't really recommend any of the others without more info.

I used to say this to all of my customers (when I was in sales) and you would not belive how many of them ignored this piece of advice: RINSING is key!  Poor rinsing between stages will RUIN your anodizing process.  This is true of any process involving aluminum, beit plating or anodizing.  Rinse, rinse, then rinse again.

When cleaning aluminum (or aluminium you might say), you want to avoid anything too acidic or alkaline or you may attack the metal.  Just about anything will work, as long as it will remove the contaminants and leave the surface clean.

The nylon should not affect the piece, just as long as it does not leave any residue behind.  You may want to let the brush and scourer soak in some of the cleaner for several hours, then rinse them.  This should leach any harmful plasticizers and such from the plastic, reducing the chance for contamination of the workpiece.

Just make sure you get a good De-ox/de-smut on the part before you anodize it.

As for GP, I've never heard of it.  Many newer "high-tech" shops are using anodes made from special Al.  Check out this site for more info on special cathodes.