I'm on 4.3e my wiiflow and cfg works fine, I only use priiloader to recover from bricks. Am not using any priiloader hacks or settings (except move disc channel).
This is what I do to install wiiflow and cfg USB loaders.
Make sure all iOSes above 200 are NOT stubbed.
I installed cios 236 (and install and patch iOS 36 using either multimod manager or wiimod), custom iOS installer to install cios 36 and 57 (must use cios 249 as base as with most homebrew) and yawmm or mmm to install the skyward sword essential wads and cfg/wiiflow channel wads. That usually works for me.