You can go the Savage Species rout when it comes to the big HD and hp change:
First no longer having a Con. the character loses any Con bonus or penalty to hit points, saving throws, and skills.
When one becomes a lich all there HD becomes d12s, and rather then rerolling all the characters HD again just add +4hp/d4 that they may have had, +3hp/d6, +2/d8 and 1hp/d10 and that should make the character 100% by the rules.
"In addition to the above, the player also wants to design a corpse using the corpsecrafter feat from Libris Mortis to enhance a body that he can take over thus giving himself a bonus to str and hp. Anybody see any rules issue with this?"
If I had a player that wanted to do that I might even alow them to add the feat benefits too there own body as they complete the magics that make them a lich in the first place, but thats just me. If they wanted to change bodys after the fact of becoming a lich I don' believe I would allow that, but if they get a nice healthy living body before becoming a lich well thats another story. hehehe