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See Part Two below to see whether your income qualifies for the Idaho Retirement Benefit Deduction.   You may find this information in TurboTax Online, in the Idaho state income tax return, at the screen Retirement Annuity, click Learn more.   Idaho Retirement Benefit Deduction   The Idaho Retirement Benefit Deduction lowers your taxable income up to $48,216 ($72,324 if married filing jointly). To qualify, you need to meet both age/disability rules and receive eligible retirement benefits. Here's what you need to know:   Part One - Age, Disability, and Filing Status   You must meet one of the following: - Be age 65 or older, OR - Be age 62 or older and classified as disabled.   What counts as disabled:   - You're recognized as disabled by the Social Security Administration, Railroad Retirement Board, or Office of Management and Budget. - You're a veteran with:  - A 10% or more service-connected disability, OR  - A nonservice-connected disability pension. - You have a doctor-certified permanent disability and it won't improve.   If you are married, you must file jointly to qualify.  If you are an unmarried surviving spouse earning qualifying survivor benefits, you may also qualify.   Part Two - Qualified Retirement Benefits  Your retirement income must come from one of these sources:  Civil Service Employees: Retirement benefits from the U.S. Civil Service Retirement System (CSRS), Foreign Service Retirement and Disability System (FSRDS), or their offset programs qualify if you became eligible before 1984. Benefits paid under the Federal Employees Retirement System (FERS) don't qualify.    If you received a CSA-1099, check the first digit of your account number:    - Digits 0-4 = CSRS benefits and qualify. - Digits 7 or 9 = FERS benefits, so they don't qualify. - Digit 8 = Look at your Notice of Annuity Adjustment to see how much comes from CSRS. Only CSRS amounts qualify.    Idaho Firefighters:     If your retirement benefits came from PERSI's Firefighters Retirement Fund (FRF), they might qualify. Look at your 1099-R for the FRF designation in your account number. Benefits from the PERSI Base Plan don't qualify.    Idaho Police Officers:    - Benefits paid from city police retirement funds closed to new members before 2012 might qualify, including retirement systems managed by PERSI for police officers not covered by Social Security.  - Examples include retirement funds for Coeur d'Alene, Lewiston, Pocatello, or the old Idaho Falls Police Retirement Fund (IFP). Check your 1099-R for the IFP designation. - Benefits from the PERSI Base Plan don't qualify.    Railroad Disability Pensions: Disability pensions under the Railroad Retirement Act might qualify. If you're under the minimum retirement age, these payments may be reported as wages on Form 1040 or 1040-SR, Line 1, rather than on RRB-1099 or RRB-1099-R.    Retired Service Members: Military retirement benefits qualify if:    - You're classified as disabled, OR - You're age 62 or older, OR - You're under age 62, worked during the year, and earned enough to file a federal return.    To claim this deduction, you need to meet both the age/disability rules in Part One and receive qualifying retirement benefits from Part Two.      

The MO Home Disaster Tax Credit is designed to reimburse you for out of pocket insurance costs after a major disaster. The maximum amount you can claim is $5,000 per taxpayer. If your deductible was $2k, that would be the cap for your credit. This credit reduces your MO tax bill and is not refundable. You can carry it over up to 29 years.   You need to file Form 5926 regarding the disaster and Form MO-TC and list HDC for the credit along with insurance documentation showing your deductible paid.   MO Homestead Disaster Tax Credit states: Eligible Applicants You incurred an insurance deductible during the calendar year 2025 for damage to your primary residence (homestead). The damage was caused by a disaster for which the Governor of Missouri requested a presidential disaster declaration in 2025. See Presidential Disaster Declaration section below. The homestead was used for all tax and legal purposes. You lived at your residence for more than six months prior to the disaster. The insurance company is licensed in the state of Missouri. Procedures to Claim the Credit The individual taxpayer claiming the tax credit shall file a signed affidavit Form 5926 Homestead Disaster Tax Credit Affidavit with their individual income tax return, verifying: Address including county of residence that suffered damage Date the disaster occurred Evidence the insurance deductible was incurred as a result of a claim paid under a homeowner’s or renter’s insurance policy issued by an insurance company licensed in Missouri. The taxpayer should also attach the document provided by the insurance company and Form MO-TC Miscellaneous Income Tax Credits.

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.