1. how can i get from raicho to there in the early morning and how long does it take and how much does it cost?No idea where "Raicho" is, but if it's at Norikura Kogen, you'll have to take the bus down to the visitor center/parking lot and then pick up a Matsumoto bound bus. At best, this will probably take 2 hours.
https://www.alpico.co.jp/en/timetable/matsumoto/r-takayama-matsumoto/From Matsumoto, you'll have to take a train to either Nagiso or Nakatsugawa. An express will take 1 1/4 hours. A local takes almost 3 hours. Not all expresses stop at Nagiso or Nakatsugawa so you may have to wait. Check hyperdia.com.
The bus is shorter from the train station at Nagiso to Tsumago, or you can also walk this section. If you take the train to Nakatsugawa, you should take the bus, which is right in front of the station, up to Magome. It will drop you off in the parking lot at the base of the town. You then just walk up through Magome and continue out the other end. Sometimes you can be on the road a bit before you get to the Pass with the tea house and vending machines. From there, it turns into a real trail through the woods until you get close to Tsumago, and you start following small roads again.
2. is it better to do the trail from nagiso to nakatsugawa or otherwise?Nakatsugawa to Magome is a steep climb and it's best to take the bus, even going downhill as it's a bit of a distance. Nagiso to Tsumago is a nice walk through the countryside, but is easiest if you go from Tsumago to Nagiso, as the directions aren't as clear in reverse. Tsumago to Magome has a bit more uphill than the reverse direction.
3. where can i stay at magome or nakatsugawa? I've stayed at the Silk Hotel in Nakatsugawa, but if you look on Agoda or even just Google Maps, you can spot plenty of hotels and ryokan to choose from. I usually stay in Matsumoto and make Narai or Magome day trips. I actually like Narai better, as it's not as overrun by tourists as Tsumago and Magome and only has a couple of souvenir shops on the south side. I do like the trail over the Magome Pass and the waterfalls below the old guard post/tea house on the Tsumago side.
For the person driving, there are large parking lots both in Magome and Tsumago. Depending on which way you're going, you can park in one and take the bus back. The parking lots in Magome are more obvious as they're right next to the road. Tsumago's lots are near the river and there are several of different sizes as I remember.
