Hopefully the 3 main switches are stackable. Simply stack them, RSTP won't cause any issues if the network is loop free, so I wouldn't worry about touching that.
Use a pair of cables to the fourth switch, and combine them into a channel using LACP.
Ports that go to devices should be configured as access ports. Ports between switches should be configured as trunk ports.
I would tend to connect each MX250 to a different single switch (one MX to one MS, and the other MX to a different MS), to maintain everything loop free.