My recommendation is always to do an inspection before you have your offer submitted to the bank. That way, you know you are submitting a 'fair' offer that does not need further negotiation.
In most cases, though not all, the sellers of a short sale property are selling the home 'as is' because finances are so tight that they can't afford to make fixes to the home or offer you money to do so.
I would talk with your buyers agent to see what he/she suggests in your situation.
You have to figure out if the price justifies the repairs needed to be done.
You can do a Request For Repairs but most likely it will be denied. Since the seller is doing a short sale, they most likely don't have the money to do the repairs and the short sale lender(s) most likely will not approve the repairs (meaning, they won't pay for them).
Check with your Realtor on how to handle that situation.
By the way, have you confirmed that you're really paying "market price"? Usually, people go after short sales because they're trying to get a bargain. I hope your Realtor ran comps on the property to make sure you were getting a good value.
Hope that helps.