I am sorry to hear about the fertility trouble. That can become emotionally taxing, and sometimes financially taxing as well. If you end up using medical assistance, techniques such as IVF can run into the tens of thousands of dollars per child born (and that's real costs, not fake inflated price tags used for insurance negotiation purposes). There are cheaper and lower impact techniques out there, which are appropriate in some cases, but IVF is a realistic worst-case scenario for many couples facing fertility problems. Also, in many states and in many health plans, fertility treatments aren't covered, and even routes such as adoption can cost thousands in legal fees. Bottom line: I hope and pray you can avoid all that.
As for investing the house fund: The conventional wisdom is to favor stability and liquidity for money you intend to spend within the next 5 or so years. And I think that's right. Getting into the weeds for a moment on optimizing your tax advantaged accounts: For house savings in regular accounts, your credit union rate is not much lower than what you'd get on a short-term tax-free muni fund; on the numbers you'd be ahead with moving that cash into something like VWSUX (yielding 1.16% tax free), but given your moderate tax rate a taxable short term corporate fund may even be a bit better after tax. Still, the credit union rate is good for that sort of account, and if the deposit guarantee helps you sleep at night then stick with it, no regrets. Within your Roth accounts, where taxes can be ignored, don't even bother looking at muni funds: any "shadow" house money can be invested in a short term corporate bond fund like VSCSX, which yields 2.28% -- enough in my view to make it worth stomaching the small but non-zero price volatility of such a fund. And while pulling principal out of a Roth early is not the best thing, it still beats forgoing the contribution entirely, which is what your current option is -- at least the 2.28% per year of earnings will stay in there until you retire, and if you don't end up needing to pull out quite as much as you thought, even better for your retirement! Think of your current strategy as contributing the max each January, investing most of that sum in a money market fund that returns 0.01%, and then automatically withdrawing an amount each December equal to the amount of unused capacity that you habitually let go each year ($8,000 or whatever), even though you aren't buying a house just yet. You're sticking that $8,000 withdrawal in a taxable cash account just so it can sit there. Don't you feel extra silly pulling a stunt like that?
And when the time comes, I'd suggest "trading" (in your mind) the cash emergency fund for bond fund savings in the Roth. That is, if you have $60,000 in short term assets in regular accounts and $35,000 in your Roth (and a record of $35,000 in Roth principal contributions), I would advise AGAINST spending $50,000 from regular and $35,000 from Roth to make your down payment (leaving $10,000 in a savings account as your "emergency fund"). Rather, I would suggest spending all $60,000 from the regular account, and $25,000 from the Roth, leaving your $10,000 emergency money invested in short term bonds in the Roth until your cash emergency fund is replenished, at which point you can re-balance that cash into a conventional retirement portfolio (such as 60/40 split between stock and long-term bond indexes). If life continues as normal, you don't permanently lose space in your Roth; if an emergency strikes at that time, the money will be there in your Roth and you can take it out tax free.
As for hunting down those unaccounted shadow expenses: There are plenty of apps and websites and programs recommended in the forums here -- things people find useful for real-time expense tracking. Mint and You Need a Budget (YNAB) are popular. I'd also look again at your automotive spending. At 17,000 miles per year on the not-very-old but fairly sensible cars that you drive (although the CR-V is a bit silly), your all-in costs should be in the $8,000 to $9,000 range -- fifty cents a mile is a very good rule of thumb based on IRS studies into appropriate business travel deduction rates. That figure is meant to account for fuel, insurance, depreciation / replacement reserve, maintenance (oil changes, tire changes, brake pads), car washes and everything else. But in your budget I only see $1,500 in fuel, $1,300 in insurance and up to $3,900 in replacement reserve (how much of that is really vacation money, though?), which adds up to $6,700 per year or less. So I'd guess there's $2,000 to $4,000 per year in hidden automotive costs baked into your lifestyle somewhere or another.
If your wife's commute is only 10 minutes, it might make sense to trade the CR-V for a Vespa (if her commute is confined to slower local roads), or at least a 7 to 9 year old Civic to match the 5 year old one. The proprietor of this site would suggest plain old biking for her commute, but being in swampy Florida (I once lived in SoFla) and with her trying to get pregnant I'll give you a free pass on that. There's at least $10,000 to $12,000 of value depreciating on your driveway in the form of that late-model CR-V, and if you replaced it with a sightly more modest $3,500 piece of depreciating machinery (a somewhat older Civic) you could make a nice sized one-off contribution to your house fund and probably knock a few grand off your ongoing yearly expenses, which might give you enough headroom to fully max out your 403(b) -- a goal worth considering. For my part, I drive around in a 20 year old station wagon bought used a few years back at a three figure price tag (and I do a fair bit of the maintenance myself), despite also having a six-figure family income. But I'm widely regarded as slightly nuts, so I try to make the advice I dispense to others a little bit more comfortable and mainstream than the choices I'd make myself. Civics are very reliable cars, so take your time, pick a well-maintained one, get it checked out by an independent mechanic, set aside an extra $500 to $1,000 to replace some of the older parts during the first year of ownership, and I'm sure you'll come out well ahead.
Also, when estimating you taxes, you're better off looking for an online calculator to estimate your liability, rather than using the overly simplified calculation you present in your post. On the one hand, only your marginal income is taxed at 25% -- most of your earnings will be taxed at a lower rate (the first $20,800, being your two personal exemptions plus the standard deduction for a couple, is effectively taxed at a 0% rate), so your income tax estimate is overly high. On the other hand, you also have to consider employee-side payroll / social security taxes (6.2%) on top of income taxes, which isn't yet in your calculation. Net-net, I would estimate your family's income and payroll taxes as being $3,000 to $5,000 lower than the ~$30,000 you calculate. Which means there are a few other hidden expenses to ferret out!
And again -- good luck on starting a family! We're rooting for you...