Hello Allenwilliams42 and thank you for your service.
Since your retro is back to 2006 and some back to 2010, the calculations will have to be done for each year based on the authorized disability rate as well as effective dates.
Reference the clothing allowance, I would submit an appeal and let it go to BVA for a decision.
As far as submitting the NOD, you can submit them now if you have already received the written decision letter explaining the increase; however, if I was in your position, I would not submit my NOD just yet and let them my retro paid to me first, keeping in mind that you have 1 year from the decision to submit the NOD; so if they (VA) says the retro will take 4-6 months to process, that leaves you with about 6 months to submit the NOD. The reason I would do it this way is if the NOD is submitted before the retro is complete, it may just hold up the retro until the NOD is finally adjudicated (just my opinion), so if you feel as though you can wait another 12, 24, or even 36 months to get the retro, you should file it promptly.
Again, the above is just my opinions based on the information you provided and what I would do in a similar situation.