Hopefully I can answer a few questions for you here.
First off, the cost. I recently just bought a 2005 999 "S", but I was also considering a brand new 2005 base model 999 because the dealers are blowing these out below MSRP. These are virtually identical to the 2006's. I would recommend going the route of a 2005 because the dealers seem to be wanting to blow these out the door. The cost of these sem to be around $16,500. The deal I was looking at was $19,000 for a 2005 999 with a full termi pipe, a PCIII, new rear sprocket, and dyno tuning. I opted for the used "S" (with 1,500 miles) and that came with a pipe and sprocket, and I couldn't be happier with the bike. As far as power numbers, I'm not sure, but the thing screams...esp. more than the 2004 749 that I came from.
Now a days, I am not sure about what models come as a biposto or monoposto, but I have seen on ebay a lot of subframes to change a bip to a monoposto. Those have run from around $150-$400. Allt he parts and plastics, used, will run about $400- $600 total. If you have any general mechanical experience, you should be able to complete the swap fairly easy.
As far as the costs of maintenance, I know you said you do 99% of the work yourself, but what you would be looking at for service from the dealer is as follows
600 mile - Approx $300
3500 mile Oil Change - $65.00
6000 mile Service - Approx $750- $800
9500 mile oil change - $60.00
12,000 mile service - $1,100 - $1,200
Also, you might want to factor in about $300 - $350 for new tires (including installation) every 3,000 - 4,000 miles, depending on how hard you ride and how soft of tires you use.
I hope this answers the majority of your questions. Best of luck.