quote PortageKeeper: "the pack then doesn't fit well in the canoe"
Not after any confrontation, gear choices are personaly based.
I have never had trouble fitting full framed and internal framed pack in the solos I have owned. Wenonah Moccasin and now an Advantage and have used a CampTrails Torrid2 internal, Peak One framed (old style RamFlex2), even an aluminum framed Camptrails. Currently I use a GG Nimbus Access and GG Nimbus Core both drop right in between the gunnels. All these packs while taller than portage style packs are narrower and largely shallower allowing them to lay below the gunnel. The OP mentioned a CCS food pack and sleeping bag on top, 23 inches plus the diameter of the bag. Sure seems like it would fit fine laying down behind the seat.
Biggest concern I would have is the weight capacity of the pack and suspension, assuming it is loaded with gear adding the weight of a canoe may not be doable.
For the boots, ShoeGoo, worked well sealing and getting extra years out of my old ankle fit Burlys. Clean them well and remove old hardened pieces (if any), not pretty but held well.
butthead