Hi your post sounded familiar. I also had Nortons and the Paso I bought 3 years ago was my first Duc. It was also a fixer upper.
Here's my advice:
1. Change the belts, check the valve clearance, change oil and filter. K&N makes a replacement filter part# KN-153. The valves are not much more difficult than a Commando, but you have to check the closing clearance go to
http://www.ducatigarage.com for an explanation on how to do it or take it to a Ducati dealer. Coming from Brit bikes be ready for sticker shock on service costs.
2. Keep the Mikunis, they are FAR better than the original Weber. I converted mine to Mikuni and highly recommend it.
3. The Michelins are the only 16" tires that are readily available. Go with them for your first year or at least your first 3500 miles. There is a conversion to 17" wheels that can be done. It takes a bit of work and money to pull off. It depends on your riding style etc. My opinion on this is, if you really are concerned with the extra speed etc the 17s will give you, buy a new 999 and it will solve itself.
4. The electrics are the weak part of this bike, nowhere near as bad as an old Commando though. There are several upgrades I'd recommend: new coils, relay mod for the keyswitch and lights.
5. Parts become available on EBAY, you just need to watch it. Body work is expensive and hard to find especially LH mirrors. If yours is in good shape treat it like gold, it is worth about $250-300.
Finally, I like my Paso more than any of the Commandos that I had. I ride it more and it always turns heads. My only disappointment is that I notice that, unlike Nortons where a basketcase would be resurrected to make a good bike, I witness many good fully functional Pasos dismantled for parts. Generally, they are worth more in pieces than whole.
If you need any other help that I might be able to help with, send me a message. There are some other guys that are much more familiar with these bikes and Ducatis than I am, but since I thought our experience would be similar I thought I'd send you a reply, good luck. Are you in the States?
Doug