I smashed the magnets in an outrunner a few years ago. I bought all new ones and had the same sort of issues...keeping the magnets in place until the epoxy set up was initially a giant pain. Multiple tries later, my solution was to use stainless steel hose clamps and tooth picks. Stainless has very low ferrous content so the magnets are not attracted to it very much.
At the time I used regular JB weld which has some amount of iron content in it. This created it's own oddities while trying to place magnets since the JB weld wanted to flow onto the magnets. The iron content is still very low and had no effect on the motor that I could determine. About a year ago, I discovered Marine JB weld. It's a good bit stronger and more resilient than the regular or quik stuff and it has no iron in it. None of the JB weld varieties are conductive that I can tell. My DMM can read up to 30 meg ohms...effectively infinitely high resistance on my meter in the liquid or solid state. Even just the "iron" had infinite resistance all by itself. Next time I'd use Marine JB weld.
Something I'd like to try is spraying the inside of the bell with electrical paint to create a thin insulating layer so the magnets are electrically isolated from each other. Skin effect over the magnets does create some amount of losses in a motor. This is also the purpose of using segmented magnets in a motor. I think eliminating any electrical path between the magnets could help to reduce the skin effect too. However, I have quite a few motors and none of them have electrically isolated magnets.
Anyway, I turned the hose clamps inside out. This puts the screw feed inside the "loop". Crank the screw outward to fill the entire bell ID. This also applies outward clamping force on the magnets. My magnets were 55mm long so I needed 2 hose clamps; one either end of the magnets. As you add another magnet turn the screw inwards just enough for another magnet to slide into place. I used regular (slow) JB weld since it took a little while to get all 14 magnets into place. I added a popsicle stick to bridge the gap for the reverse curve under the screw feeds
I coated the ID of the bell in epoxy and then put wax paper over it where the hose clamps would mash into the epoxy. That helped to keep the epoxy in place and NOT get all over the hose clamps, but it was not perfect. By the time I was done the hose clamps still had epoxy on them. Once the JB weld got pretty solid...enough to not ooze around, I pulled out the hose clamps and then removed all the excess.
I discovered a trick about JB weld...
Cold JB weld is quite thick and cures very slowly. It's also not very gooey and sticky. You can mix up a fresh, uncured batch, freeze it and hold it in your fingers. Hot JB weld gets quite runny, gooey and super sticky. When it cools off again, it cures rapidly.
What I did in 15 easy steps:
1. Make sure the ID of the bell is perfectly clean. Clean all the magnets. You want good bonding.
2. Coat the interior of the bell in room temperature JB weld. You want about a 1/16" thick layer. Enough to completely fill any gaps behind the magnets
3. Stick the bell and magnets in the freezer. You want the JB weld really thick.
4. You want to keep everything cold until all the magnets are in place. I did it in my cold garage which was 40-50F.
5. Use the hose clamps to hold the magnets in place. At first your magnets will be crooked and not aligned well. This is OK. Just get all the magnets in place under the hose clamps.
6. Your hands will warm up the magnets, bell and epoxy...stick it back in the freezer to keep things cold.
7. Once all the magnets are in place, space them evenly apart and vertical in the bell. I used round tooth picks as spacers. They needed to be pushed in place with a little effort, but were exactly the right fit between the magnets to hold them snugly.
8. Give the hose clamps another turn or two outwards to really get them tight against the magnets and to push out all the extra JB weld behind the magnets.
9. Now that everything is "locked in place", bring the bell in out of the cold. let it warm up to room temperature. The epoxy will get much softer. See if you can tighten the hose clamps on the magnets a bit more with out anything moving.
10. Set it in your oven on it's lowest setting. Get out some aluminum foil to catch the JB Weld drips. Put the bell in the oven for 20 minutes. You should see the extra JB Weld start dripping off the bell. This serves 3 purposes. Hot JB weld bonds better to things, the extra JB Weld should drip off the bell and heat gets the curing reaction into high gear.
11. Set the bell on the counter to cool off slowly. The epoxy ought to take maybe 5-10 minutes to get pretty solid. You can test it's hardness with a tooth pick.
12. Once you are confident the epoxy wont move anymore, but is not fully set up, remove the hose clamps.
13. With an exacto knife, tooth pics or some plastic implement, start removing the spacer tooth picks and any excess epoxy that is NOT under the magnets. Be careful to NOT move the magnets so they don't come loose! The JB weld will be super thick and some what crumbly. It will come out from between the magnets like thick putty and can be cut with with a razor blade.
14. Let the motor bell set for a couple of hours so the epoxy can finish curing.
15. Put your motor back together.
Note: Removing the excess epoxy is about maintaining balance in the bell and reducing weight. Without precision equipment that can tell you how the bell is out of balance, the best you can do is not leave extra weight in places that will create imbalances. IE: Remove all the extra epoxy so the bell is as light as possible and has no heavy spots in it.