What are the best sites to for a beginner to learn? - When there is a topic I need information on, just google it and start there. There are quite a lot of sites that provide very specific information, then there are the general sites.
In terms of lenses, should I get a cheap prime or just stick with what I have? - With your all in one - stick to that, then look at the images that you have taken in terms of their focal length. That will tell you what you are interested in and help point to the lenses that would hold you interest.
Is there anything else I should get that I can get on a budget? (ie. tripod, other lenses, etc.) - I started out with a $10 special. Did not use it the first year, a bit in the second, more in the third, quite a bit from there out, until it broke. Then I wound up spending a small fortune on a nice one with a great head. I knew what I wanted and what I would use.
How long should I wait before upgrading to a kx or kr? - For me it was about 4 years between the K100 and K20. Then I felt guilty. I have bypassed the K7 and K5 up till now. I may get a K5 when its replacement is announced, since I can use the high DR for the evening landscapes that I take.