Why is it these things go unnoticed for so long. We "just found out" that some of the indirect paper that is coming in has "interest will accrue on a 360 day..." language in the note, but the Fed box is calculated on a 365. (Which is our accrual method).

This is in the borrowers favor, but should we have new docs drawn up and executed to fix?

If you are certain the fed box disclosure is based on 365 & your system is accruing on 365 also.
Then you have actually underdisclosed in the Box and you should be o.k. Also, given the large amounts for vehic loans today and the longer terms the difference should be fairly insignificant = I would guess 50 - 75 cents per month ==> $50 over a 60 month loan.
I would not attempt to re-document and "fix"; I would
1. Sample the portfolio you have to verify the Fed Box is 365 & your system is 365 & the notes term says "360".
2. Check the APRs to verify they are underdisclosed
3. Show how you are preventing the problem going forward

Before paying any attention to TILA disclosures, you must reconcile the contract with your business practice. If the contract calls for an actual/360 accrual basis and you are not abiding by this requirement, then you need to either a) change your accrual method to match the contract, or b) amend the contract so it matches your accrual method. Since your intention was to use the more consumer-friendly actual/365 accrual basis, then you will probably choose to inform affected borrowers that you are unilaterally amending the note to memorialize what you have already been doing. Until you modify the note, your TIL disclosures are wrong if they do not reflect the less favorable accrual basis because that is the legal obligation between the parties.

Before announcing the contractual change, determine whether the contracted repayment schedule causes the loan to pay to $0.00 when interest is calculated using the amended basis. If the schedule is no longer accurate, it too must be modified. Assuming the basis change is in the borrower's favor, the payment change should also be in the borrower's favor.

After you have verified or revised the payment schedule required by the contract, then you can proceed with APR and FC testing.

What we discovered is that the software that several of our dealers are using had the 360 in the "Promise to Pay" portion of the contract, but the TIL box was calculating based on a 365, which is what we use for our consumer portfolio. We have pointed this out to the software vendor and they are fixing the program for the dealers that use thier program.

Payment schedule is amortizing correctly based on the 365.

As long as you have actual/360 in the contract as your interest basis, the TIL disclosures should be based on actual/360. It doesn't matter how the contract came to read that way, or that you actually do something else--Section 226.17(c)(1) requires you to base all disclosures on the "legal obligation between the parties", i.e., the note. Since all the payment amounts are based on actual/365, and you intended for that to be in the note, and you service the loans that way, you should discuss with bank counsel the simplest and lowest risk way to amend affected loans so their notes agree with your disclosures and servicing practices. Fixing the system will prevent future violations, but not those in the past.