Swells on the open sea are rarely a problem - and on their own are not going to be a problem vis a vis your transom cutout.
However you are dealing with the Columbia Bar, and here a high swell can turn nasty, especially on a strong ebb.
We crossed that bar some years ago with a largish swell, and they were impressive over the bar. But it was a calm day otherwise and it went fine.
A wind-driven wave train against the river flow can, as you know, create hellish conditions. Wait for a good weather window and talk to the locals that know. In our experience the USCG will not advise you whether to go or not. They'll give the prevailing conditions and leave you to decide for yourself.
1984 Fast/Nicholson 345 "FastForward"
".. there is much you could do at sea with common sense.. and very little you could do without it.."
Capt G E Ericson (from "The Cruel Sea" by Nicholas Monsarrat)