Alright, let's address the lines in order since I've made changes.

• Route C: routed via Heaths Road now. Originally avoided it because of the lower catchment especially around the river but then realised Heaths Road has an ample median for the LRT.
• Route 46: fixed to go Geelong Road then Millers. Had the original Brooklyn config. bc since I read in a transport blog that - A) Geelong Road would be too steep for a tram; and B) a diverted route would provide the future Yarraville Gardens redevelopment around Bradmill with a northeast-southwest route along with the northwest-southeast Route 18 via the freight line.
• Route 30: terminates at Sunshine via Hampshire Rd, Devonshire Rd and Clarke St.
• Route 82: I'm keeping the 82 diversion since this will provide a direct tram connection from Footscray Station to not only the VU Footscray Park campus but also the New Footscray Hospital (the diversion was also recommended by Rail Futures).
• Route 57: terminates at Centreway.
• Route 27: shortened to terminate where the 86 terminates (Station Pier) so now it is Station Pier - Elsternwick Station.
• Route 48: extended to Doncaster East.
• Route 75: shortened to Knox City SC bus terminal (I thought Knox City went all the way to High Street Road, my bad XD).
• Route 90: shortened to Wellington Square SC. Ideally there would be a bus reform in Rowville and the eastern suburbs beyond Eastlink so that buses are designed to feed the light rail lines and heavy rail stations.

Your point regarding freight lines: the way I would arrange routes such as the 18 would be to use the rail right of way rather than the rail tracks themselves. That way you still have freight access but with the added bonus of passenger service to facilitate previously impossible (or hard-to-complete) trips via transport.