Portaging - Portages are always usually hassle. Finding a good take-out and put in point, getting my chair out and getting over fences etc is always a bit of a nightmare. We always try to paddle through locks where possible. This sometimes takes a bit of lock-keeper blagging, but we've found most of them really helpful.
Transfers- Boat ramps, baeches and pontoons are ideal, however, sometimes not possible. I had to do some scary put ins and chair-canoe transfers on the Mississippi. The following picture required a 'leap of faith' from my chair to the canoe after my friends had got me down a 45 degree boulder bank.