The issue of internal training is a huge one, and there's been an ongoing discussion for the last few years across various websites, including here at aikiweb, e-budo, and aikidojournal.
Like I said, check out the "Non-Aikido" forum here, that's where most of the "internal" discussion goes down. Check out Ellis Amdur's blog over at Aikido Journal, he has a couple things to say about the place of this type of training in Aikido. Look up stuff about Akuzawa and/or the Aunkai (there's a current thread about a recent seminar of his in the "Non-Aikido" forum). Lastly, look up threads by Mike Sigman and Dan Harden. They have some good things to say, but be warned that their threads are a mixed bag, they tend to run into a lot of "personality clashes".
There are a couple of threads you should look up:
How to teach and train relaxation
Training the Body for Martial Movement
& Training the Body, Part2: Exercises
(this one is a HUGE, mixed bag, it has a few really good things to say, but you have to wade through pages and pages of crap to get at it)