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So, I soldered it all back together again, leaving the pit in the waffle board as pictured above. I did proper joints rather than test tacking as the desoldering gun works very well with leaded solder and its slightly lower melting point. I put the boards back in, bolted the power board down with fresh heatsink paste, double and triple checked all the connections and the aux battery voltage (has been a while) crossed fingers, toes and every other imaginable appendage, and switched on.

...

...

It worked. No smoke, just all the normal charging noises. It pulled 12A @ 240V and did just what it was meant to. After three hours  my imiev is now at 100% battery again.

Next move is to pull it out again, tidy up the waffle board and fill the pit, solder it together again, quickly test and then repot the main board. Haven't quite decided whether to try installing another cap to replace the cremated one or just to leave well enough alone.

One very happy (and more than a little relieved) iMiev hacker here.