That Experience Jpn fare can be hard to get for many of the ITM>NRT flights, esp on short notice. And even with Experience Jpn fare, the cost/hassle/time involved with any plane ride involving either KIX or HND would negate any advantage that flying would have over train, for OP's purpose. On the other hand, ITM is fairly easy and cheap to get to from Kyoto using the limo bus. If I were the OP and flying out of NRT, I would definitely take the train from Kyoto>NRT, unless you can fly cheap from ITM>NRT.

If your home is SEA and you don't mind the drive to YVR, then I would price out fares from YVR. There is a seasonal service from YVR>KIX (not sure if you're traveling during that season). For Jpn and HKG, recently I'm finding that YVR fares are almost always substantially cheaper than SEA. To me, driving's a major hassle. But the price difference is so much that I'll be driving to and flying out of YVR for every one of my 3 upcoming trips to Jpn/HKG over the next 6 months (actually, one of those trips is flying out of SEA but flying back to YVR, then renting a car to drive back down to SEA).

Otherwise, what abmj-jr said. It's ~4hr by train from NRT to Kyoto, but the train ride is comfortable and it takes you right to the city center.