Whilst it would have been easier to mask, it is what it is and your steps forward make sense. I know what is like to take a step forward then find that an earlier step would have made life easier.

I do my own powder coating, in case you get more done here is how I mask of bits...
I use aluminium foil for most bits, cheap and easy to use. I often remove the bigger aluminium bits prior to curing. For more intricate bits I have heat proof tape that will not effect the curing. In your case I would get your guy to do his sand blasting the return for masking.

On the cracking, I bet you have thought of this already, you might find that using a fine dremel grinder or similar tip to make a sharp clean edge first up and taking time move out from the edge before you get a bigger tip would be ok. I would say the most important bit is to avoid fracturing the coating. Given that it tends to bond I think it will work just takes time.

On the rusting the shafts are bright steel so I think it wont be too bad, I put CRC or similar stuff on the metal and use that to avoid rust. On the castings I think most of your clean up is inside and will be covered with grease.
Put up some pics when you get em cleaned off. They will look awesome im sure.

If you do find its taking to long, consider getting another set and mask them up, cleaning off the parts with sand blasting to recoat is common but might be risky due to risk of damaging the surface. I bet your powder coater used sand blasting prior to coating to get a clean surface. Check with him as you might find that you can mask of what you want to keep coated and sand blast the rest off.

Also have you checked on effect of curing in relation to effecting the heat curing of the axles... exposure at that high temp might effect their strength. I have not elected to powder coat my axles for fear of effecting strength, if you found some info on that I would be interested.