I tried to figure out a way to do this effectively for years (until I moved much closer to the city
). I have a mate in Boronia who says that Canterbury Road is the answer, but I stuck with either Highbury Road, or trying to stay close to the Glen Waverley railway line.
The way I eventually found best was to follow Blind Creek path to Shepherd's Bush, and then go straight up Wheelers Hill to Glen Waverley station from there. From Glen Waverley, I'd use a combination of backstreets and paths to get to Gardiners path trail and then into the city from there. Highbury Road is much more direct, but I found it more dangerous / difficult to get there initially.
Whichever way I tried, it always seemed too dangerous and too far out of the way, but now that High Street Road is safer, that might be much easier. (I used to live just off HSR). I'm just glad to now live somewhere better served by cycle friendly roads.
Hope the bike commuting goes well for you!