I've ridden from Carrum Downs to Mornington virtually completely off-road several times, although the bit I used to ride from Pines Flora & Fauna Reserve through to Cranbourne Rd was the easement for the freeway. The new path takes the fun out of it.
You can also ride from Frankston to Baxter on the Baxter Trail, alongside the Stony Point rail line. I haven't investigated the exact links, but it meets the Peninsula Link Trail somewhere near where the railway passes over the freeway just south of Cranbourne Rd.
From Baxter station, follow the old rail line along, firstly with the line on your left, then at Frankston-Flinders Rd, cross both the road and the rail line & continue along. The section Frankston-Flinders & Moorooduc Rds is quite low, and can get very wet in winter, requiring you to take to the rail line itself to bypass the bogholes. Crossing Moorooduc Rd can be a difficult affair, but should be easier since the new freeway should have taken a lot of the traffic off it. Cross the track again to get around Moorrooduc station, then pick up the trail past the station carpark, then follow it all the way to Mornington.
The trail, informal as it is, is best ridden on a MTB, but in good conditions could be ridden on a cross bike. I have no knowledge of any plans to formalise the trail link, however there is talk (again not confirmed) of the Tourist Railway extending services to Baxter, which would at least partially explain why a bridge was built over the currently disused section of line when the freeway was put through.