Indeed the custom textures you added got messed up (I unpacked the brres for yoshi, saw all the normal outfits... but the one swapped was distorted as in your screenshot). But (using the exact folder you sent me) ran step2 again and it seemed to work.
Couple questions: What operating system are you on? Have you attempted to run step 2 again since then?
<semi-technical-ramblings>The last time I've seen such an error was when I was making the CUPASH modification itself. For some reason Vista skipped copying a few bytes out of the tpl files (basically, the 1st conversion an image goes through) resulting in an offset image (the blinds you speak of). I thought I had fixed that by writing an alternative to tplsplitter (the modification of step2.pl) but it seems to not work in your case.</semi-technical-ramblings>
I'm not entirely sure where it went wrong when you made it... I'll have to go through and examine the hex and see what is wrong at that level. I'd assume it was a one-time glitch if it only affected one custom... but for all of them? That's a little weird. I'm willing to try trouble shooting it for ya, but it may take a bit. (I'll pass on the files to VILE too, he is a bit more into hex matters)
Oh wow... that's some impressive messup. All of them appear like that?
Could you send me your common5 (the new one) and one of the brres files it generates?
Hell... if you can, zip your entire cupash folder. I'm curious, I've only managed this type of error once (I offset some data while manually messing around with the hex).
Might want to work on the shading. (For most stuff I do... I just use color modifications, overlays and such to keep the original shading mostly intact)
You don't really need the iso any more for texture hacks (use the SD loader), just the music hacks still require it.
Basically...
To make texture hacks: ASH (+TexConv, + NTcompress --- they ARE downloadable in the FAQ... just hidden --- but not very well) Texture PACs (also downloadable from the topic)
Music Hacks: (Read the FAQ --- specifically the music one by Vyse --- I've never done it) Need WiiScrubber to put it back onto the ISO (in above FAQ) Need to load the iso somehow (Backup loader or USB Loader, mentioned in FAQ)