Hi Chase,
I added manual hubs a few weeks ago, and also found that they don't fit under my stock wheels (in my case, 2003 SE 16" 6-spokes). However, luckily for me, I'm currently in "winter mode" running 1st gen Tacoma steelies (Toyota wheels on a Nissan...shhhh! ) which fit over the hubs fine. I picked these up with tires on Craigslist for super cheap, so you never know - there may be a cheap enough set on there.
I wouldn't recommend trying spacers...I think they'd have to be like 3" or 4" thick to push the wheel far enough out to clear the hubs.
You might be able to bore the stock wheels out to fit, but I'd be worried that would weaken the wheels... From looking at my stock wheels, I figured you'd need to take maybe a 1/2" on material off the bore, which seemed like a lot to me. Might not be a problem, just my two cents.
Sorry, I'm not sure about the hub bore size. Just was hoping to add another point of view. Good luck, and I hope you find an answer...otherwise I'll be stuck when I go to put my summers back on!