At 45k a year, you should be able to have more money after all of your savings than just the 5000 roth max. so I'd say you should be able to accumulate your down payment without needing to withdraw the principal of your roth.
So two paths, that came to mind right away:
You can just open up a taxable vanguard account, and invest in there. This way it'll most likely grow. Only drawback, a lot of people are saying there's a bubble right now, so if the stocks tank, you might end up with less than you had before. Or if it grows, you'll obviously be hit with taxes. But that's all a personal preference and/or gamble that only you can really decide.
If it were me, and with the short, 3 year time-frame you're looking at; I'd probably keep that in the highest interest bank account I could get. Yeah, you won't be getting as much growth, but its guaranteed not to go away either. Which may give you some piece of mind, if buying a house in 3 years is a "must-have" goal for you.
(I (as does MMM) use capitalone360. It has a .75% interest rate, which is 4 times higher than any credit union or bank I've been able to find. Also, great customer service. Here's my refer a friend link, if you need it.
https://r.capitalone360.com/fvMaBF6sbX If you use the link, and open with like 250, you'll get 20 and I'll get 20, I believe. Please don't feel like I'm pushing you towards my link though. In fact, I think MMM has a bit better of a sign-on bonus somewhere on his blog. Either way, use a sign-up bonus, because FREE MONEY!)
So after that, if you have anything after your IRA contributions and savings towards your down payment and/or after your pay bump, I'd open up a taxable vanguard account, put it into the total stock market index, and just let it sit/keep contributing, but not withdrawing unless an emergency.
Good luck!