On your last day (Porth Colmon to Bangor), your track shows avoiding main roads until Penygroes, where it picks up the A487 into Bangor. Given that you've deliberately avoided the A499, taking the A487 isn't a good idea. The traffic is much much heavier on the A487 than the A499 and there is a traffic free cycle path alternative. When you get to Penygroes, follow signs for NCN route 8, which is the old railway line into Caernarfon. You can pick it up from the Inigo Jones slateworks if you wish (by the roundabout North of Penygroes*).
In Caernarfon, to join the off orad routes together, you need to go around the castle, then into a car park next to the Victoria Dock (by the Morrisons) to rejoin the path. This will take you all the way to Y Felinheli; I would really really advise against the A487 from Caernarfon to Bangor. I'm a fan of main roads, but that one isn't worth the time saving, unless you intend to ride over 20mph, or you fell your right arm is surplus to requirements.
I wouldn't go up the hill toward the hospital in Bangor either - there's roadworks by the hospital this week and next week. There's a traffic free path from Y Felinheli to Bangor Tesco alongside the A487 which totally avoids the hill anyway. From the shopping park, the road into Bangor is quite tame.
* As a total alternative, I'd actually suggest continuing on the A499 past Clynnog Fawr, and turning left toward Llandwrog about 3 miles further on. From there, take a right in Llandwrog and follow the road through Saron and over a bridge before turning left towards Y Foryd nature reserve. It's a lovely ride alongside the coast to Caernarfon castle.
