Welcome to the forum, CantGrow. It looks like you're doing fine.
I am an E5, just hit 8 years TIS, but I have a warrant package in right now. I was at 18% roth tsp, but I am going to bump it up to 20 or 21% since I just got my TIS raise this month. I do 100% of my contributions as roth. I have never worried about taxes before, just looked forward to getting my refund. I just got married too, so I really have no clue what our taxes are going to be like. I guess this is something I could look into. Also, my wife is extremely investment-risk adverse, she would be most comfortable if I kept all of our cash in a savings account or under the mattress, that is a battle I fight from time to time.
If you know roughly when you expect to buy the house then you could stash your down-payment fund in an equity index fund (>10 years) or a short-term bond fund (5-10 years) or CDs (<5 years). Move the fund to the less-risky assets as you approach your date. The key is not chasing yield by taking on excessive volatility risk or principal risk. When you're finally ready to buy then the down-payment fund gives you more negotiating power for discounts, and that price reduction makes up for a whole lot of 1.2% APY CDs.
I wouldn't buy a home on active duty, even if I intended to retire there. Living in your retirement location gives you several years to research the neighborhoods and wait patiently for bargains. Going to open houses and home shows 1-2x/month helps you refine your criteria, and the practice pays off when you see a place because you'll quickly recognize your dream home at the right price. Read Jane Hodges' "Rent vs Own" for a more balanced perspective on that perpetual debate.
As for your spouse, I think "risk averse" is a synonym for "volatility" and "risk of loss". If she can teach herself to not look at the statements then you can invest in a moderately aggressive asset allocation-- because you have a military income. So maybe she would agree to let you handle the paperwork and she only looks at the numbers once or twice per year. If you're living on one income and regularly investing the other income, then when the market drops she can take the Buffett attitude of cheering for cheap index-fund shares on sale.
What would you guys be recommending for an "emergency fund" and does this really need to be separate from my "savings account". Bearing in mind that I am military, and my job is extremely stable, and we don't rely on my wife's income to pay any of our bills? I've never been debt free before, so figuring out what to do with cash is kind of a "first world problem" for me.
You could put enough in the emergency fund for a car repair or a no-notice plane ticket to visit family during an emergency. With a military income (plus her income), $5K could be all you need in your emergency fund. You'd put the immediate expense on a credit card and then pay it off out of the emergency fund or out of next month's income. It might cause you to skip a month or two of contributions to a Roth IRA or a taxable account while you pay off the card and rebuild the emergency fund, but that's how it's supposed to work.
You could put the $5K in a savings account, or a money-market account with NFCU or PenFed. You could put it into a three-year CD and hope that you don't have to break the CD. You could even consider your Roth IRA contribution an emergency fund. You're allowed to withdraw those from your account at any time for any reason with no taxes (you've already paid tax on a Roth contribution) and no penalties. Of course withdrawing the money from the Roth means it's not compounding for you, but some workers choose to do this because it makes them think really hard about what expenses qualify for an emergency.