Retirement tax questions

No.  You don't get taxed on the gains or losses in IRA accounts.  You get taxed on the whole distribution as regular income tax (over your basis if any).  The basis is any non deductible contributions you made.  So when you convert to a ROTH the whole amount is taxable.  

If you have realized losses in your taxable accounts you can deduct up to 3,000 on your tax return after any gains.  The rest you have to carry over to next year.  So at least 3,000 will reduce your income and conversion.