120,000km A5

"and bonding them to the shell of the rotor."

That's what I was thinking too... it's a glue binding the magnets in place to the rotor. 

Curious to research if this can be repaired "As-New" again.

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I had a closer look at the magnets and can't see anything significant missing. There are some marks on the magnet edges but I suspect this happened as the broken pieces of plastic came off and no doubt spun around for a while before exiting. I will try and get some advice from an auto electrician on what could be done to rectify. Interestingly the FSM (disassembly-engine, alternator rotor pg 86) has 4 photos of the rotor, 2 don't appear to have any material on the magnet edges, 2 do - hmmm.

Meanwhile I have tried tackling the water pump. Despite lots of penetrating oil and lots of wiggling over several days, the impeller wasn't coming off the shaft (yes had removed the circlip). As the cylinder is off, I was able to undo bolt at far end of impeller shaft and take shaft out with impeller still attached - now soaking with penetrating oil from the other side as still can't get it to budge and may leave it stuck - the rubber seal and sealing seat in the impeller look fine. But what I saw past the mechanical seal retainer didn't look so good (first photo) so off that came. The space between retainer and oil seal in cylinder was full of gritty crud and excess gasket compound (second photo) and the drain hole well blocked (third photo). The FSM says this drain hole should not be blocked, "if it does, the coolant may mix with engine oil". Ok, this cavity has an oil seal on the inner side and a liquid gasket sealed retainer on the outer side - doesn't either or both have to fail for oil and coolant to mix? And how did all this crud get in there?? After clearing the drain hole thought I would see where it goes. It exits the cylinder block (forth photo) just above and outside the crankcases, in the front of the engine, directly in line to catch all the shit from the front wheel. I can only think the crud has come up the drain hole. Mental note; don't pressure wash front of the engine near the drain hole exit! 

The mechanical seal looks ok and actuates nicely. However I would like to give it a good clean without taking it apart - should I use solvent, coolant, plain water or just a squirt with compressed air? Plenty of cleaning to do while waiting for a new TC17317 oil seal.

You ask about the drain  hole plugged and the possibility of coolant going in the crankcase- The lipseal can only hold pressure in one direction. Pressure coming from the backside of a lipseal will lift the seal face and allow that pressure past the seal face. The job of this lipseal is to keep the oil in the crankcase. The job of the mechanical seal is to keep the antifreeze in the coolant circuit. If either seal fails, the drain port is there to relieve the pressure between the 2 seals so that both seals don't fail. We call it a telltale hole be cause if we see any fluid coming from it, we know we have a problem to fix.

For the record, my latest adventure with my rebuild - the crud build up was possibly 2 times greater  than yours. I've never seen a seal cavity with so much crud. It destroyed the water pump shaft and I'm now going to make a new shaft out of 304 stainless right after I  finish refurbing  the cylinder liners ( in progress)

Update on the generator rotor. Advice from auto electrician was, do not try to remove magnets, "you will never get them back on ever!!!". Recommended a tidy up and use a good expoxy resin to the areas necessary. So removed the remaining bits (first photo) and was very tempted to stop there given first couple of photos on page 86 of FSM. However all subsequent photos of the rotor in the manual show bond on the edge. Kawasaki frequently changed/upgraded parts even within a given model year (as I found out when restoring my '73 Z1). Checked part numbers and rotor had same number for A1, A2 & A3, 21007-1015 but this changed to 21007-1048 for A4 & A5. May not mean anything but I decided the bond on the edge was probably there for a reason - oil less likely to be caught on lip of rotor and work between magnets and casing? better oil flow? don't know. Anyway decided to break out the JB Weld and tried to replicate (second photo). Time will tell.