Keep three bases, but make the travel days light
Use two nights in Skopje, two in Ohrid and one in Bitola before returning to Skopje. That gives Matka its own day, leaves a full lake day in Ohrid and avoids treating Bitola as a photograph between two coaches. Day six should remain a return and departure-buffer day rather than another long excursion.
The plan works best when the Skopje to Ohrid and Ohrid to Bitola coaches are chosen before the rooms become non-refundable. For Bitola to Skopje, compare the current coach and rail departures and choose the one that leaves a safe onward margin. Each station-to-room transfer belongs in the schedule.
Use weather to choose the outdoor day
Matka, a lake outing from Ohrid and Pelister all compete for suitable conditions. This six-day route has room for Matka and one Ohrid outing, not every outdoor possibility. If Matka has poor weather, keep the day in Skopje. If the lake is unsuitable, spend more time in Ohrid's old town. Pelister needs extra time and transport, so add it only by extending the Bitola stay.
Shorten without damaging the route
With five days, remove Bitola and return from Ohrid to Skopje. With four, keep one full Skopje day, one Matka or city-flex day and two nights in Ohrid. Do not shorten by taking a late road arrival into Ohrid and an early departure the next morning.
The total below is an adjustable example for the stated assumptions. Airport travel, boats, mountain guides and any international connection sit outside it.