It's funny how parallel some of our projects / solutions run. I just assembled the same clutch shoes and was going to tell you I found a way to make the springs fit, I just put the whole spring in the jaws of a pair of pliers and squeezed it to put more bend in the main "finger" that holds the clutch shoe, now it lies flat.
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Like you, I found them nearly impossible to apply even with a clutch tool. I stuck a screw through the clutch shoe and spring and used the same pliers to move the "leg" a bit further back.
The intended orientation for the clutch nut is with the groove further away from the engine, it looks like you may have done that already. Kyosho's
tapered clutch nut is meant to make installation easier, though in my experience it only helps a little.
I think those
shoulder bolts from my other Fish build,
way back would be the perfect solution to your shaft-end/bearing issue. I'll probably wind up using another couple myself in these builds.
M3 thread, 5mm long, 5mm diameter shoulder x 5mm long.
I've got a dozen, I'll mail you a few if you have trouble finding them locally.
I've thought of dremeling a deeper groove, for the 2-piece clutches too, because I've noticed the outside of that spring starting to wear while the shoes still had plenty of "meat" on them.
I would want to make some sort of jig to get the depth right and also not widen the grooves by mistake, and then also weigh the shoes afterward to within .01g to avoid imbalance.
I wonder if at high-enough RPM's, those "wraparound" style springs might actually lift out of their groove and stretch to the inner diameter of the clutch bell as a result of the centripetal force, potentially snapping them - I had one recently fail and it's encouraging me to try and move away from the "semicircle" style clutches entirely. Kyosho uses 2x shoes from a 3-shoe set on their FW-06, pretty effective in my opinion.
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Edit: I just worked out that at 35k RPM, there's 13,000 G's of outwards force on the clutch shoes; a 2g shoe experiences 60lbs of pull! (sorry for the metric/imperial mashup) Those wraparound 2-piece clutches are probably fine below 30k RPM, but over that I want the spring & shoe type.
The Kyosho clutch shoes don't have a deeper groove, but the springs are perfectly contoured to them.
Since some of my clutch bells are the last of their stock or otherwise irreplaceable, I might run only teflon/composite shoes in them rather than aluminum to try and maximize their life even if I have to rebuild the clutch more often.