As you say, fly cutter is unbalanced which is bad for the spindle bearings, but more importantly because the fly cutter is such a large diameter it has to be run at a low rpm. I often use them on the mill when I want a nice finish, does take a long time. Used one on your ballnut mounts and possibly the motor mounts, can't remember. Anyway, I tried it once on my router, about 40mm diameter, just out of interest. It worked, but the finish wasn't consistent. The spindle doesn't have enough torque at such low rpm, so I switched to a 1/2" 2 flute endmill and that's much better. I wouldn't go above that size on aluminium. For wood, or surfacing the bed certainly use something bigger.

Collet nut... I have emailed 5 different eBay sellers about those asking if they are balanced and therefore suitable for use an a 24,000rpm spindle. Asked about the standard nots and the ones with bearings in (though I doubt they're suitable) and only 3 replied. All said no they're not suitable. So I'm a bit stuck now :(
The ones you linked to are type M, not type A which is what's used on the spindle:

http://www.ebay.co.uk/itm/3x-ER20-Ty...ht_2141wt_1037

I didn't receive a reply from that eBay seller... so no idea! Can't see the drilled bit to balance them on the picture, but that's obviously inconclusive.

I wonder if these are more expensive because they're balanced, or because they're sold in the USA:
http://www.ebay.co.uk/itm/ER20-ER-20...item4cecb838f0