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If some portion of the distribution went to state tax withholding, this portion can be included on line 5a of Schedule A.  TurboTax will do this automatically upon entering the Form 1099-R if your itemized deductions exceed the standard deduction.  Federal tax withholding is not deductible on your federal tax return, but might be deductible on some state tax returns (Alabama, Missouri and Oregon).

That is correct it does include the 2024 payment made in 2025, except TT is reducing the total deductible state and local payment on Schedule A by an allocated amount calculated using the 2024 refund on the State and Local Income Tax Refund Worksheet, Part I.

You have already identified the issue.  Now you need to "annualize" your income, or accept the "option to do the calculation quarterly by entering income from each quarter".  That will match your one time Q-3 income with the Q-3 payment you made.  If you don't annualize your income and report income and payments by quarter, the IRS, the states, and TurboTax assume your income and tax payments were made pro rata in equal amounts each quarter.  And as you pointed out, the tax payments in Q1 and Q2 weren't enough to cover a portion of the Q-3 one time income. 

In 2026, the codes used will allow the 2025 amount to be tax free since you did include it in your 2025 return even though the payment of the required minimum distribution (RMD) was paid late. It will likely be Code P. See the list of codes for 2025 which will be updated for 2026. What do all the codes in Box 7, Form 1099-R mean? @angela829 

You must remember that NY taxes full income and then allocates the tax. Therefore, the full NY deduction is taken on the full NY income Line 32 NY AGI Line 33 should be calculating your standard or itemized deduction on NY terms. No allocating Line 35 dependent exemption is taken in full Line 36 is the taxable NY income Line 38 - the program will look up the state tax for you TurboTax does the work so you don't have to! You are very smart to be asking questions and understanding how it all works. Great job!

  ,  you raise an interesting situation/point:(a) Section 911 of the code  defines foreign earned income as :The term (A)In general The term “Foreign Earned Income” with respect to any individual means the amount received by such individual from sources within a foreign country or countries which constitute earned income attributable to services performed by such individual during the period. Thus implying local entity payment, except for US Govt. or any of its depts. Note  however, that a tax payer acting as self-employed, working at his foreign tax home, can receive  payment from an US entity and this would be eligible for FEIE ---- No W-2, or 1099. This would need to be reported on Schedule-C, Schedule-SE and subject to local tax laws.   (b) IRS also generally holds that  income is sourced  to the location where  work is actually performed.   thus  your earnings  for the work performed in country X  ( which country please ? )  should mean  that the remuneration should be sourced  to that  host  ( tax-home ) country and therefore eligible  for  foreign earned income exclusion. (c) However, my confusion here is that you were still employed by the US entity and paid by them.  You probably did not pay any taxes to the host country.   So is this foreign earned income ? (d) In the old days when I was on foreign assignment, I got  paid partly by my US employer  ( and on W-2 ) and partly by the local entity ( a Wholey owned subsidiary/ local entity ),  paid taxes  to the host country and therefore  the foreign portion of the income/ housing / COLA etc. were all eligible for FEIE. (e) Also my understanding, while hazy, is that when on sabbatical, a prof gets paid ( and continues to have employee benefits ) by the "mother" entity but may receive grants/stipends etc. from the host institution.  If that is your case then that portion of earned income definitely would be  Foreign income.   Any details of your situation may help clear up this --so please help