Great job so far - keep up the saving! Hopefully other forum contributors will see this, and add something...
There are plenty of numbers / charts, etc that show how tax sheltered accounts win over taxable accounts in the long term - and at 25, you should have a long-term perspective.
As for having 12 months CASH EF on-hand in a savings account, you're losing 2%/year to inflation.
Recommend cutting back to 6 months CASH EF, or put it in a money market account with Vanguard to give more flexibility.
Also, as your income increases over the years, you will find that you may be able to max out all your pre-tax accounts, and will need to have a taxable account to contribute to, so recommend you keep it around. I recommend people attack their savings plans in a specific order (below).
In your case, you're already maxing your 401k. So I'd recommend starting by funding a Roth IRA account at Vanguard (independent of your Roth 401K) by contributing $5,500/year from your taxable account. As your income increases over the years, you may become ineligible to contribute fully and/or directly to a Roth IRA, so start it while you can, and the contributions + capital gains increase tax-free.
1) Max out your 401K contribution to get the dual benefit of saving pre-tax dollars, and reducing taxable income.
2) Max out your HSA account (must have a HDHP to have an HSA account).
http://www.madfientist.com/ultimate-retirement-account/3) Max out a T-IRA or ROTH IRA contribution. Since your income is currently DOWN, start a Roth IRA independent of your Roth 401K.
4) Invest in a taxable account. (you already have one, and want to move $5,500 from this account into a Roth IRA)
Hope this helps!