So your wife has a 401(k) and a 401(a)? Does she get an employer match for both accounts, or just the 401(a), or can she choose which account to take the match?
Contributions to a 401(a) work like this:
* Employer contributions, and earnings, are tax-deferred. You won't pay taxes on them until withdrawal. Similar to Traditional 401(k).
* Employee contributions are, as you noted, after-tax (note: some 401(a) plans allow for pre-tax employee contributions. Maybe she has a choice?). When you withdraw, you won't pay taxes on these contributions (under current law) so this is similar to a Roth 401(k).
* To answer your main question, employee contributions to a 401(a) do not count toward your $5,000 annual contribution limit to an IRA (Roth or Traditional).
* I'm not certain, but I suspect that your wife can contribute at most $17,000 combined to her 401(a) and 401(k). EG, $10,000 to 401(k) and $7,000 to 401(a).
I think your best bet is:
* IF she only gets employer match in the 401(a) option, then contribute to the maximum to get the match. If she can get a match based on contributions to either 401(k) or 401(a), then choose which option is better for you. (Hint: for most people, you're better off with tax-deferred over Roth because you're likely to have a period in your life when you'll be in a lower tax bracket when you take distributions.)
* If you can invest more, then put your next $5,000 into an IRA, either Roth or deductible Traditional (if eligible based on income limits). Choose Roth or deductible Traditional (if eligible) based on your personal tax considerations.
* If you can invest more, than invest to the maximum $17,000 in 401(a) or 401(k) or a combination. If you are looking to lower current taxes, then favor traditional 401(k).
* If you can still save more, than add investments in a taxable account.
Now that you're married, ensure that your combined accounts make up a coherent total portfolio that reflects your desired asset allocation and goals. Don't look a each account as its own portfolio, look at the complete package.