Well...
What you have is perfectly fine to load the ISOs themselves, from your backup loader.
In addition, Wad2ISO allows you to specify what IOS to start Triiforce in, so you could launch the forwarder ISO with one and the forwarder ISO can, in turn, launch the actual games with another.
By default, you should just use d2x for everthing but there are a few games I tried that do not work with d2x (there are others, mostly VC N64 & NeoGeo not listed below):
N64 Zelda Majora's Mask
N64 Paper Mario
N64 Super Smash Bros.
WW Moto Heroz
For these, you need to have 38rev17 installed to another slot (I use 247, but it doesn't matter which). Then, when creating ISO's for these games, specify slot 247 for launching, or whatever slot you chose. There are other games that don't work with d2x but are minority, so you might want to skip this step altogether if all of the games you care about load fine with d2x and you don't want to be bothered. You definitely don't want to set everything to load from 38rev17, as you will lose a lot of compatibility, as well as the ability to play online on the WiiWare games.