I think that you are wise to address these issues now. Most people who work at a keyboard all day will eventually develop some degree of discomfort and the sooner it's addressed the better.
The Truly Ergonomic keyboard has a good build and is split some, which helps reduce ulnar deviation. Beware however, they have a lousy track record responding to complaints.
If you are willing to assemble it yourself, the ErgoDox is an excellent choice. If you're creative, it allows you to customize the split, spacing and tenting. Remapping keys is a big plus.
Although I have never used one, the Kinesis Advantage seems to have a lot going for it. I have been modifying an ErgoDox and the more I change it, the more it resembles the Advantage. There are many faithful Advantage users here and I've heard the company's support is outstanding. If you don't want to bother with a kit, the Advantage may be your best choice.
Some who didn't want to change to a different layout found an inexpensive solution in the Kinesis freestyle or the Gold touch. At under $100 it is possible solution. The switches aren't mechanical.
I have personally found the combination of an ergonomic keyboard, adjustable tray and adjustable chair have greatly helped me. See my ergonomic journey here.
http://flic.kr/s/aHsjFazJhh