Welcome to Just Answer. I am here to help you resolve your tax and finance concerns. Please feel free to ask anytime you need extra help.
First I need to advise you that it too late to file an amended return for 2008. That deadline expired on April 15, 2012.
You should have reflected the interest and dividends as income on your return as well as the capital loss. The loss would not be entirely usable on the 2008 return since there is a $3,000 limit for the net deductible capital loss.The remainder carries over for future use, year by year.
As to the failure by UBS to reflect the tax paid on your 1099-R that will require correspondence between you and the IRS to get resolved since UBS is not able to assist at this time. Include a cover letter explaining this and a copy of your year end statement from UBS to show the tax paid. The IRS will allow this due to the circumstances or provide you the time to secure a corrected 1099-R.
The IRS will make all other changes to the return and send you a letter showing their final changes. Be sure to mention the interest, dividends and capital loss in your correspondence so all these items can be corrected.
You should also check your tax returns for the following years to be sure the capital loss carry over has been reflected on Schedule D so that you do not lose this tax benefit. You can still amend 2009, 2010, and 2011 using form 1040X and its attachments. These forms are available at www.irs.gov You will also need to notify your state about the final IRS changes to 2008 and file amended state returns if any changes are made using the 1040X.