Hi Dean et al,
I'll second the advice on cardio. I would also look into some weight training, focusing on total body stuff like cleans. I think everyone here agrees, unless you need to focus on an area that is weak, isolation exercises are only good if you want to be a body builder.
For your sword training I would spend a lot of time doing shomen cuts paying close attention to making the cuts as straight as you can. Slow down and make sure each one has perfect form and you have good breath/kiai. Some people have said 1,000 cut per day for three years will teach you the meaning of swordsmanship (see blog here: http://www.geocities.com/kendosuburi/
). I think doing about 300-500 is good enough for most of us non-kendo/former kendo players. 100 cuts even done at a slow pace go by in just a few min.
I also like sumo shiko, leg stomps (I only do about 100 per day, although Konishiki I read sugested 300-500 per day). The Nihon Sumo Kyokai has put together an exercise program for non-rikishi to follow here: http://www.sumo.or.jp/eng/kyokai/kenko_taiso.html
Lots of good stuff here.
I think if you can learn a little zazen or chigung to learn some good breathing methods to tie it all together you'll be doing well and you should be able to keep up with your peers in the dojo.