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Good to hear Distilled on this one Thanks Mike!

I'm pretty sure that if it's a 301 permanent server-side redirect, than it will be seen in analytics as direct traffic. However in the past I've seen a lot of talk about Google seeing the original source of traffic in the first place with the 301 being hidden, but I've had experiences like your talking about and I do believe it's direct. Would love to hear some other SEO brains on this lol.

Yes I saw the same thing. I than took the site and implemented a similar search like the old site so that I could get the pages back and internal linking the site had back in place. This seemed to help my traffic and rankings move back into place.

I would also dig into your analytics under content. Start comparing pages viewed so you can start pin-pointing what pages are dropping out of the SERPs in-case you missed any in your 301s. I recently had a situation where I did everything right but the site I was working on had an internal search that was indexable so after looking through my analytics I was able to find out where my drop in traffic was really coming from.

Like Andy said, it's still a bit soon, so give it some time and continually check up on it.