It only requires a 620 (this is an awful score) credit score to cahout refinance with the right bank or mortgage broker. Yes you can start the process now however she will have to deed the property to you at closing. She is NOT to be included as a borrower on the new loan when you refinance.
You may have problems if your debt to income ratio exceeds the 45% threshold. The ratio is calculated by totalling all month obligations listed on your credit report, plus proposed new house payment including taxes and insurance, plus any court ordered support divide that number by the gross monthly income. If the 1k monthly that you are paying for her apt is court ordered then it will count as your monthly debt. If not don't tell your bank you're paying for her apt.
Hopefully the appraisal is less than what you think its worth because them you could reduce the amount of buyout.Most banks have there own internal overlays to conventional loan guidelines which is published by fannie Mae, therefore you may first want to confirm the minimum score to qualify. Because CA is a community property state they may require her to be on title to the property at closing so the deed to you may have to take place after closing. In exchange she revives her buyout which can be held in escrow until she deeds her ownership interest to you.
There is usually a "due on sale" clause in the note with the bank and this means that if any owner of the property sells their interest in the property then the bank can call the note or demand full payment. Because of this you may want to wait until your divorce is final to remove her from title. However most banks will not exercise this clause because they don't want your property they want the interest earned on your loan.
http://WWW.brokeroutpost.com is a good place to find a lender if you're credit has blemishises.