Build two servers or buy one from manufacturer?

I'd go for the one machine from a reputable supplier, for the following reasons:

• Although you plan on having one machine "as a spare" now, I will bet you my firstborn that you will come under extreme pressure from your management to "make use of all that expensive computer gubbins", so that it won't be a spare for very long. When either of those machines break, you then won't have any warranty support or spare parts availability and you'll be down for a lot longer than four hours.
• A standard machine with a standard support contract is better for continuity reasons. Sure, you know how to build, rebuild, and fix hardware, but is that a "required" attribute for whoever they hire to replace you when you go under a bus, win the lottery, or get headhunted to Goopplesoft? Homebrew hardware is a hand grenade for anyone else who has to work in the environment you created; do them a favour and leave the pin in.
• The build quality of the major manufacturers, especially in hard-to-evaluate anciliaries like rails, mounting hardware, fans, and power supplies, is almost certainly better than anything you'll be able to pick up and build yourself. I've never seen anything that comes close to Dell's rails, for instance, or the DRAC/iLO type stuff from the majors. It doesn't seem like much, but the frustration factor those sorts of things can save once you get used to them can be significant.
• Your time isn't free. Those hours you spend putting it all together will be hours that the school district is paying you for, and that's time that could be used to fix other problems or do other useful work.

I can live with 4 hour downtime, but it will not be comfortable. Am I better off buying or building? I see pro's and con's both ways.

The costs you save on parts will most likely be cheaper due to quality and/or poor support. From RAID cards to memory and power supplies, saving a few bucks here and there is usually a losing battle in the end. If that end happens to be 7 months away to 7 years, people's opinion of "the end" tends to be more of a matter of luck when rolling your own servers.

I only really need one server (I'll use VMware esxi), but if I build I will build two identical machines to make up for lack of a support contract.

Well, you haven't addressed shared storage so having two ESXi servers (w/o shared stored) is no different than having one server. How is this a benefit? Personally, I'd rather have one beefer server with quality hardware vs. two cheap machines and no shared storage.

Slightly off-topic: if you're going the VMWare route, in my experience VMWare is much more 'picky' when it comes to nVidia chipsets for AMD Opterons. Granted you could be going with Intel but if cost is such a factor, I would highly recommend AMD from a cost perspective. I don't know if you're dead-set on ESX/ESXi, but if not I recommend Citrix XenServer 5.5. With more features for their free version right out of the box and overall less cost in terms of pricing for enterprise-y features, give them a look. Especially for education where every damn dollar matters. I would avoid going the VMWare route for cost and cost alone. Just my two cents.

What do I need to be considering most, and what am I potentially missing?

I've answered a similar question to what you're posting (here). I'll cover my 3 main points I brought up in terms of what you're missing from server level hardware. Womble covered a lot of points that I'm reiterating so feel free to skip to the bottom.

1. Durability - Granted not everyone has an identical experience but server grade equipment seems to last a bit longer than their desktop counterparts. But even for prolonged (and stressful) usage, server hardware tends to hold up to the demands under the specifications provided by the manufacturer.

2. Stability/Reliability/Longer support Usually better driver support for the appropriate OS. Desktop equipment may or may not have solid drivers but server hardware wouldn't sell without some serious attention to detail. Driver support is critical as well as serious testing of equipment. I find that once I pay for the server hardware, I worry less about this issue. If an issue does arise, manufacturers usually update the drivers/firmware/software/etc.

3. Scalable - The majority of most core server hardware (motherboards, CPU, RAM) anticipate upgrades to one degree or another. Most desktops do not anticipate a larger quantity of resources. This is usually a function of the motherboard chipset more than anything, but server chipsets are significantly different from desktops.

What you're missing

You're missing out on better hardware/software (drivers) from vendors with tons of experience and lessons learned baked into their products. Not to mention the typically seamless upgrade paths (scaling-up) to management features, server vendors have tremendous added value that you just simply can't build by yourself.

You're missing out on components that when combined together tilts the probability of failure away from your server. Whether you realize it or not, you're adding more workload to your responsibilities that really aren't furthering the school district needs and under-utilizing your time to the fullest. And that means that the school district is missing out on your attention for more important tasks.

What you need to consider

I have built servers over the years for myself and a handful of clients. These days, I find myself recommending/emphasizing that my clients go to a vendor (HP, Dell, Sun, etc.) for the quality of parts that I cannot obtain or for the support contracts. Support contracts seem wasteful/meaningless but to me they're kind of like insurance: you only appreciate it when you need it.

Previous almost-identical questions here and here.

If it were me, I'd get an HP (or Dell or IBM or whatever you prefer) server to get all the benefits of a well-engineered system, then build up my own white-box server to use as a backup.

You could also go half way and use a 2nd tier server brand like ASUS or Intel servers. What you get is the case, power supplies(s), motherboard, cooling system, and often the iLOM or iKVM. What you have to supply or get is: CPU, RAM, and storage. And of course install those items in the server yourself.

We've used the ASUS 2U RS520 Xeon 'Nehalem' with ESXi and been happy so far. We're also using them OpenSolaris and Hyper-V. We've also used Intel's servers the same way.

This will save you money, but you have to put in your time to choose components that will properly for you. Both Intel and ASUS are ESXi tested, etc, but your configuration will be up to you to make it work. If you are good at systems configuration, then this is not so hard.

It depends what you have more of, time or money. If you have more time than money get two servers. Just make sure to spend enough time researching parts before you order. Also stick to 'server grade' parts. Intel motherboards, supermicro motherboards, ECC ram, LSI or 3ware raid cards, 'enterprise' or RAID edition hard drives cost more for a reason!

But if you don't feel completely comfortable doing it, just buy a Dell or HP. Just make sure to call them and talk to them on the phone before placing the order- you can often get better discounts by talking directly to a sales rep.

I'm in agreement with the idea of using a known quantity, i.e Dell, HP, etc.

At the end of the day, your job is to be an enabler of the "business". IT is never looked at as a profit center (because we don't directly add to the revenue or profits) but If you're spending half a day tracking down a local source for a mobo for a custom built machine then you're going to quickly be scrutinized as to your value to the organization as a whole and someone is going to question the soundness of your decision to "go cowboy" with the hardware. You'll pay more for a Dell or an HP or a "whatever" but having a replacement part or tech support a phone call away and having a certified tech on site replacing faulty equipment is going to be invaluable in keeping things humming and keeping your "customer" happy.