You have tabled three good options in your question. Now, consider the following:
1) Is there an alternative property that meets your needs (alternate supply)?
2) How long is your planned occupancy period (the longer this period the lower the risk of equity loss)?
3) How much higher will your loan rate increase if you pull out of this deal and what will be the monthly increase (rate are moving up)?
4) Do you have time for a 2nd Appraisal?
5) Are you in a position to take advantage of both the Fed/CA Tax credits (are you positioning to get the combo $18K)?
If I were in your shoes and making the decision (obviously without the benefit of answers above) I would move forward in this order of preference:
1) Ask for sales price to be lowered to appraised value.
2) Split difference 50/50 or X/X (remember that the lender loans on the lesser of appraised value & contract price).
3) Request a Closing Cost Credit to shave off some cost.
4) Make up the difference, close, and start enjoying your new home!