You have a great idea to eliminate the batteries from under the bonnet. Using an ultracap would allow you to use a thinner gauge of wire to the batteries in the rear. The car should handle better having the weight more evenly distributed.
Failing this, buy a section of Mylar for insulation. It isn't conductive and does a great job at thermal insulation (and is dirt cheap).
I assume the TDI has glowplugs? If so, you could easily over-run the ability of the supercaps to supply them and then start the high compression motor.
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