i would NOT do it before P2V, simply for the fact that an upgrade/repair install might break your current system. Also with virtual machines you can snapshot before doing the upgrade/repair so you always have a fallback.
to answer the original question, you will have to do the repair install from within windows, booting the cd will not allow the upgrade.
best bet though is to do clean installations and restore whatever you can restore. P2V and doing a repair/upgrade is a serious risk. don't forget to patch up windows again after performing this install.
