Hum, seeing you talk about buying basketcases, you caught my attention. 
Currently I own five ST1300s. I have two '04s, '06, '10 & '12. I also owned, as my first ST1300, a '05 that I put 174.3K miles on.
The '05 & '12 were new when I bought them, the others were all wrecks, except the '06 which is truly a "basketcase"!
It's not cheap restoring any of the sport touring machines due to the price of the plastic, but one nice thing about the ST1300s, they were built from 2003 (2002 in Europe) until 2012 (USA, Europe/Canada went until 2014...I think) so, currently, there are plenty of available parts.
Yes, there are some differences between the '03-'07 and '08 & later. Also there are differences between the cop bikes and non cop bikes. But they all seem to have a lot of parts that are interchangeable.
None of my bikes have seen a Stealer Mechanic since my first '05, other than a couple of warranty work issues. When I decided I could screw things up no worse than the last mechanic did on that bike. That was 2008 and the bike had less than 38K on it at the time.
Since you have no qualms about doing your own work, I would suggest you going with a ST1300. Depending the mileage and condition of the 2006, I would probably swing that way too. But check the maintenance log on any bike you decide to buy.
Good luck with your decision.

Currently I own five ST1300s. I have two '04s, '06, '10 & '12. I also owned, as my first ST1300, a '05 that I put 174.3K miles on.
The '05 & '12 were new when I bought them, the others were all wrecks, except the '06 which is truly a "basketcase"!
It's not cheap restoring any of the sport touring machines due to the price of the plastic, but one nice thing about the ST1300s, they were built from 2003 (2002 in Europe) until 2012 (USA, Europe/Canada went until 2014...I think) so, currently, there are plenty of available parts.
Yes, there are some differences between the '03-'07 and '08 & later. Also there are differences between the cop bikes and non cop bikes. But they all seem to have a lot of parts that are interchangeable.
None of my bikes have seen a Stealer Mechanic since my first '05, other than a couple of warranty work issues. When I decided I could screw things up no worse than the last mechanic did on that bike. That was 2008 and the bike had less than 38K on it at the time.
Since you have no qualms about doing your own work, I would suggest you going with a ST1300. Depending the mileage and condition of the 2006, I would probably swing that way too. But check the maintenance log on any bike you decide to buy.
Good luck with your decision.