after many years of wondering I think I finally found out the difference between PD-M323 and PD-M324 recently. It turns out that in ~1997 shimano redesigned the SPD cleat slightly. They did so in a slightly weird way (for anyone, especially shimano) because they kept the same part numbers for the cleats but actually started making completely different parts with the same number on them.
The main change to the cleat was that the radius of the part that bears against the rear jaw was changed. Newer pedal designs (starting with PD-M515 I think, but I'm not sure about all models) adopted rear jaws with a larger radius. The consequence of this is that if you use first generation cleats with later pedals, you get more float (and faster wear to the cleat), alternatively if you use current cleats with a first generation pedal, you get less float (about zero in fact). Folk who have tried this combination who need float quickly abandon the arrangement as unworkable.
So PD-M323 is a first generation SPD pedal and PD-M324 is a second generation pedal, but the pedals are otherwise the same, I think. It is possible to convert a first generation pedal to a second generation pedal with some dremel tool action on the rear jaw, or perhaps by replacing it.
BTW I have heard of tolerancing problems between the cones and the (ludicrously expensive) special tool, such that the tool won't fit over the cones, because the corner radii don't match in some cases.
My money is on the crank as being a cause of problems, but you should check out the pedals (most easily done by substitution BTW).
If the bearings come adrift the normal thing is for the LH cone to wind itself inwards due to precession (whereas the RH pedal goes slack; the difference is because the cones and locknuts are RH threaded both sides). This can eventually cause all kinds of problems but in the short run a clunk as described is one of the less likely ones.
Shimano don't specify a torque setting for the cone and locknut but I suggest that
a) you torque it a bit like most other M5 threaded fasteners (NB this is a very fine pitch one) and
b) that you use some threadlock on the cone and locknut if you have the pedal apart.
If the pedal is just being adjusted, I normally don't bother with threadlock, reckoning that if problems arise they will soon be noticed (by contrast if you don't notice that your bearings need adjusting in the first place, you won't notice if they suddenly go out of adjustment, either). However if the pedal soon needs adjustment again because of precession, then threadlock is called for.
IME shimano pedal bearings using the tiny 3/32" balls can last virtually indefinitely if they are kept correctly lubricated and adjusted, but can equally wear quickly if this is not the case. In particular the balls cannot share the load properly if the adjustment is bad, so out of the saddle efforts will fairly quickly mangle everything, even if tapping along in the saddle might not.
FWIW I have taken a set of very worn PD-M515 just to see what would happen if I tried to save them. They had been run loose for some time so that they were worn such that the cones were not breaking up but were somewhat oval, so that (at best adjustment) the bearing was alternately slightly tight and slightly loose as it went round. To my surprise, after about three cycles of adjustment and regreasing (with a grease that has a high MoS2 content), the bearings started to behave themselves again; in fact I'm still using them. They have not required attention for the last 4000 miles.
cheers
