The plan is not included in the boxset. I don't know if they'll release another set with the plan included (they probably will though). As EJO said in an interview about The Plan, this will not be the last bsg movie (given the plan sells well), so even if they release a set with the plan, this will probably end up not being "absolutely everything".
Cheers Mr W, dont think i can wait that long, gonna have to go for it! For the episodes with deleted scenes, can you just watch them with the scenes included (not the special extended episodes towards the end but for all episodes) i hate watching isolated deleted scenes; it just feels so fragmented!