Cross Training routines for longer rides
One of the best ways to build up to longer rides is through interval training. 

The best book I've found on the subject is: The Time-Crunched Cyclist: Fit, Fast, and Powerful in 6 Hours a Week by Chris Carmichael. The book includes a lot of info on lactate threshold, energy metabolism, nutrition, race and century training plans, etc. I first tried out his methods after reading one of his articles in Bicycling on century training. 

Basically, Carmichael's methods are a form of interval training where you are doing things like hill-repeats, power intervals, fast pace intervals, etc. There's a lot of info out there on interval training. One of the more common is called HIIT (High Intensity Interval Training). 

FWIW - I've made interval training my primary method of training for long distance training. I did 3 centuries this summer and never did a training ride over 60 miles. Prior to 4 years ago, my mode of training for long distance was a gradual distance build-up and had mixed results. With interval training, my performance on long distance rides has improved significantly in both speed and how I feel afterwards.

"What other strength/flexibility exercises will help? (yoga, back/shoulder exercises, etc.)"

The upper back and neck can be a real problem on long rides. For this I use a regimen that I got from T-Nation called Deconstructing the Computer Guy. I've found that the exercises to alleviate insufficiencies related to sitting at a computer all day, also translate quite well to cycling. 

Revisiting...

I'm between projects at the moment so thought I'd add to this a bit more.

You asked what other aerobic exercises are best. Probably the best is something that you have accessible and will actually do. Swimming, running, walking, rowing, elliptical machines, etc are all good aerobic exercises, but you actually have to like it enough to be regular about it. 

For strength and flexibility there are plenty of options. Yoga is one; as well as things like martial arts, tai chi, etc. For strength, weight training is fine; but not a "body builder" type program. 

You specifically mentioned that you are having issues with shoulders, back and arms on your increasing distance. I mentioned an article from T-Nation above that has some great techniques for alleviating these kind of issues. (I must note that T-Nation is a rather obnoxious web site, but the advice I referenced is quite good.) For myself, I had postural and muscular imbalance problems due to cycling and too much time at the computer; and found a lot of relief in following a program very similar to the one described in Deconstructing the Computer Guy. (Four years ago I was on a century and could barely turn my head in the last 30 miles due to neck/upper back pain.) It definitely worked for me and my cycling buddy as well.

Hope this helps.