Retirement tax questions

Thank you for responding, but I think you missed some of the details of my question.

1. I did pay tax on the income, because it was a Roth contribution, not a traditional one. Therefore there shouldn't be any need to amend my 2016 tax return. But if someone can explain why I would need to do that, I'm all ears.
   
   Note that in your reference IRS Pub 525 page 10-11, under the section "Excess deferrals", subsection "Excess not distributed", it says (emphasis mine):
   
   

   If you don't take out the excess amount, you can't include it in the cost of the contract even though you included it in your income. Therefore, you're taxed twice on the excess deferral left in the plan—once when you contribute it, and again when you receive it as a distribution (unless the excess deferral was a designated Roth contribution).

   
   I'm not sure why this parenthetical exists, since in fact you still are taxed twice on designated Roth contributions as far as I can tell (see references at the bottom of my post), except that the first taxation of those contributions was just the normal income tax on those contributions since they were contributed as after-tax amounts.
2. It is too late to take a corrective distribution. It is not too late to take any distribution; it will be an out-of-service distribution, taxed and (if done before age 59 1/2) penalized by 10% as any other early distribution would be, but the amount of the excess contributions plus any earnings attributable to those contributions will be marked in the plan such that that amount must be withdrawn (and not rolled over) before any other distributions are possible, including any rollovers.
   
   Therefore it is important for me to know which plan the excess contributions are deemed to be in, because I must resolve those contributions by withdrawing them and their earnings before I am able to roll over that plan into any other plan or an IRA, whereas the other plan (not containing the excess contributions) can be rolled over freely. My 403(b) doesn't have the best investment options in it, so I am eager to resolve this excess contributions issue as soon as possible (even if I have to pay an early withdrawal penalty of a couple hundred dollars) so that I can roll it over into an IRA or into my 401(k).
   
   See 26 CFR § 1.402(g)-1(e)(8)(iii) "Distributions of excess deferrals after correction period" and 26 CFR § 1.402(g)-1(e)(8)(iv) "Distributions of excess deferrals from a designated Roth account" (emphasis mine):
   
   

   (iii) Distributions of excess deferrals after correction period. If excess deferrals (and income) for a taxable year are not distributed within the period described in paragraphs (e)(2) and (e)(3) of this section, they may only be distributed when permitted under section 401(k)(2)(B). These amounts are includible in gross income when distributed, and are treated for purposes of the distribution rules otherwise applicable to the plan as elective deferrals (and income) that were excludable from the individual's gross income under section 402(g). Thus, any amount includible in gross income for any taxable year under this section that is not distributed by April 15 of the following taxable year is not treated as an investment in the contract for purposes of section 72 and is includible in the employee's gross income when distributed from the plan. Excess deferrals that are distributed under this paragraph (e)(8)(iii) are treated as employer contributions for purposes of section 415 when they are contributed to the plan.

    

   (iv) Distributions of excess deferrals from a designated Roth account. The rules of paragraph (e)(8)(iii) of this section generally apply to distributions of excess deferrals that are designated Roth contributions and the attributable income. Thus, if a designated Roth account described in section 402A includes any excess deferrals, any distribution of amounts attributable to those excess deferrals are includible in gross income (without adjustment for any return of investment in the contract under section 72(e)(8)). In addition, such distributions cannot be qualified distributions described in section 402A(d)(2) and are not eligible rollover distributions within the meaning of section 402(c)(4). For this purpose, if a designated Roth account includes any excess deferrals, any distributions from the account are treated as attributable to those excess deferrals until the total amount distributed from the designated Roth account equals the total of such deferrals and attributable income.