Matsumoto to Magomejuku via Nakatsugawa

Can I use Suica/Pasmo to pay my fare between Matsumoto station and Nakatsugawa station?
How do I get ticket from Nakatsugawa station to Magomejuku?
Can I bring large luggage on board Magomejuku local buses?

Thanks!

Can I use Suica/Pasmo to pay my fare between Matsumoto station and Nakatsugawa station?

No, the two stations are in separate IC card areas, and IC cards cannot be used between them.

How do I get ticket from Nakatsugawa station to Magomejuku?

By buying a paper ticket at a ticket machine or ticket office.

Can I bring large luggage on board Magomejuku local buses?

I could not find any specific rules for the specific bus company, but many local bus companies ask passengers to limit their luggage to max. 10 kg bags.

Thanks!

How do I get ticket from Nakatsugawa station to Magomejuku?
No ticket for the bus is necessary - I've always paid on board with cash. I don't think I've ever seen anyone with a pre-paid ticket.
Just on the IC card question, when I do the trip from Matsumoto I use the Shinano Limited express and then back-track to Nagiso because the connections are better. Certainly for Nakatsugawa to Nagiso IC card is not available (despite the ticket gates at Nakatsugawa having IC readers in the ticket gates), and I just pay the extra few hundred yen on the train.

Indeed, IC cards are not accepted on the bus to Magome. You pay with cash on the bus, as explained here:
https://www.japan-guide.com/e/e2015.html