With wheel assemblies, as with many other similar parts of your bike, it is important to understand the nature of the mechanical assembly and how it works to avoid difficulties. The hub assembly would seem to be a very simple bunch of components - and it is - but getting it correctly assembled (on purpose) seems to send some people into a tail spin, so here is a tour.
The idea behind how our hubs are engineered is to make the front axle, the inner bearing races, and any spacers or extra bits like a speedo drive, function as a structural element of the suspension. Imagine assembling all these parts by themselves. For the front, you'd have the two fork lowers, the outside spacers, the inner bearing races and the center spacer all bolted together by the axle. Assembled loosely, you have a wobbly mess, but clamped tightly, you have a very strong and rigid connection between the two fork lowers. The larger the axle diameter (and hence, the larger inner races and spacers) the stronger and more rigid this assembly will be. which is why high performance applications have large hollow axles. This is the intent of the basic design. The wheel itself simply spins on the ball bearings located on this structure.
So when assembling the bearings into the hub, the distance between the bearings you are trying to achieve is not the space machined into the hub, but the distance the spacer that goes between the bearings locates them apart. If you were to leave the center spacer out, you could drive the bearings completely home on both sides, but then when you put the rest of the assembly together and tightened the axle you would be placing great axial pressure on the bearings causing them to fail very quickly while losing most of the structural stiffness of the assembly. The bearing seats in the hub are machined a tiny bit deeper than needed to make sure the spacer is what determines the bearing spacing and not the hub. If the spacer were even a little bit too short, the hub would hold the bearings too far apart and you would have axial compression again on the bearings leading to failure.
Proper assembly is simple. Press one bearing all the way into its seat until it hits bottom. Slide the axle in, and from the other side slide on the center spacer followed by the other bearing. This will aid tremendously in aligning up the other bearing for pressing it in. You can use the axle itself to press in the bearing if you round up enough spacers and washers and simply tighten the nut down until the center races clamp down on the center spacer. Then take the axle back out. When properly assembled, the center spacer should be a "tight slip fit" between the two center bearing races. If you end up going to far as in your case (which is not hard to do), striking the center bearing race on the opposite side will move the other bearing back out to the perfect spot. Technically, this of course is a very evil way to treat your new bearings, but in real life the impact needed will move the offending outer race with no ill effects.
So since the bearings are the only moving parts, they are the only thing that need lubrication, right? While that is true, I always coat EVERYTHING with a film of grease. While they don't move against one another, given time they will corrode and sometimes can be nearly impossible to disassemble, so a little protection is a good idea!