For both Tawang as well as Kohima you will need an ILP.
For Arunachal, the best place to get this done will be in Guwahati, if you can't find a reliable person let me know and I have an ex-army contact who can help. I would not recommend doing Tawang with an Innova, although I got there with my Swift! The roads are need a 4x4 90% of the time, and despite the great work from the BRO it is very touch and go. My drive there was in April - so expect the roads not to have changed much, but for the worse in the rains.
If you do intend on taking it all the way, please start extremely early, carry a puncture kit, and split the drive from Guwahati to Tawang in 2 stages - Guwahati - Bomdilla; Bomdilla - Tawang - you can return in 1 day. If you are lucky (dry roads, no landslides) that should work out.
I carried camping gear as well as spare fuel/water.
The Nagaland ILP is a straightforward process at the Naga House either in Guwahati or Shillong - will take you 45 minutes - 2 hours; depending on how busy the officer is.
Carry photographs and preferably passports (any other government ID should be OK, but they might ask you a few questions).
Please always stay abreast of information about the region when heading to Kohima, since you will pass Dimapur - where road blockades are common place. Just looking up things on the previous night will help. You will need to pass this on the way to Kohima.
Please note that you will need to double back to Guwahati to go from Tawang -> Kohima -> Shillong
Approximate Drive Times are:
Guwahati - Tawang - 16-24 hours - split across 2 days, uphill; 16 hours downhill.
Guwahati - Shillong - 4 hours in the day, 5 hours at night - road works in progress + rain
Guwahati - Kohima - 8 hours approx (+ 2 hours for miscellaneous issues!)
Also one more piece of advice - the chicken's neck can be very tough so please plan for some contingencies: that is the gateway to the NE - Srirampur on the Assam border, roads are under construction and sometimes leads to inexplicably long bottlenecks.
I have no experience with Thimphu. But there is a very good travelogue on that (en route to Tawang) that might be of great help.
http://www.team-bhp.com/forum/travel...an-tawang.html
PS: The NE is incredibly beautiful, and I cannot ever convey how much I want everybody to go there. If anything is a bottleneck or doubt, post away, and I will try to help you find a solution.