DId you '!Magnetize to V4' (one of the pose files with v4) the boots, and also try selecting the, Include morphs, include scales, etc. from the body properties of the boots? (Properties tab, beside the parameters tab). May help. Since the leglength in morphforms is just erc for the y scaling in thighs and shins. -0.4 sets the y scales to 94% (opened up the "edit dependencies" and watched what was happening). Or possibly adjust the scaling in the boots to match. After that I'm out of suggestions :)

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Consider me insane if you wish, but is your reality any better?