Well, I think that it goes without saying that you just need to spend some time on the bike. There is really no substitute. If you have access to a road bike that is the best way to develop aerobic capacity because it is possible to go longer at a lower heartrate. Additionally, the jarring of mountian biking has a specific effect on the body that shifts energy to the anaerobic pathways. Another option is to get some slick tires for the MTB then go for some longer rides on the pavement.
After you develop this "base" you can gradually decrease time and increase intensity with interval training, etc.
There is really no need to lift weights b/c there is no correlation between strength on the bike and strength in the weight room.
As for the stretching/flexibility, I would recommend a daily stretching routine and perhaps a yoga session once per week.
Hope this gets you rolling