By the looks of
http://www.openstreetmap.org/ it seems NCN 2 extends over a ferry from Plymouth over to Cremyll so I'd aim to take that.
From there I'd take the B3247 coast road along through Seaton, slightly north up to No Mans Land then drop into Looe (or keep along the coast but there looks to be some stairs at Millendreath if you went that way, might be easier than lots of climbing and then descending going around that bit). But I've never done this bit so I'm not sure about it, it's going to be hilly from the looks of it whichever route you take. Might want to get recommendations from someone who's actually ridden these bits.
[EDIT] From the look of Google Streetview there's quite a few stairs to get from Millendreath up to the edge of Plaidy to be able to ride into Looe. Still may be easier than the road route alternative with lots of climbing though. Depends on the load being carried.
From Looe I'd definitely head to Polruan, take the little ferry across to Fowey then B3115, A3082 and then as little of the A390 as that would require to get you into Snozzle (i.e. left and shortly right to head to Tregehan Mills to pick up NCN 3). I've done this bit during a 600km Audax (Kernow & South West) and it was fine for me. You can zoom in on the relevant bit on a map here:
https://www.strava.com/activities/240158222These are little more main roady than the NCN routes; NCN 2 starts up again half way between Fowey and St Austell but takes a pretty windy route to get there. I guess there aren't any Sustrans-y enough options between these places for there to be an NCN style route.
