Thank you. I was able to get it working correctly (it seems) today referencing the PB demo ROM. The issue was with the data at D09800, the patch adds on two bytes of something before this at D097FE and also changes/restructures a bunch of following bytes as well, while in PB you guys kept the data starting at D09800 as is, but changed just a few bytes in that data at D09803, and doing that fixed up the strange item issue which does indeed seem to be present with the patch on a clean ROM, unless somehow I'm mistaking horribly.
So for now everything seems good and working with it.
I do have a concern though that came before this issue, with something I changed in order to get it working at all for me.
Working with the debugger:
Non Flawless victory branch:
$C1/012D 22 74 D6 C0 JSL $C0D674[$C0:D674]
$C0/D674 AD 09 2D LDA $2D09 [$7E:2D09]
$C0/D677 29 0F AND #$0F
$C0/D679 F0 05 BEQ $05 [$D680]
$C0/D67B BF 6B 01 C1 LDA $C1016B,x[$C1:016B]
$C0/D67F 6B RTL
Flawless victory branch:
$C1/012D 22 74 D6 C0 JSL $C0D674[$C0:D674]
$C0/D674 AD 09 2D LDA $2D09 [$7E:2D09]
$C0/D677 29 0F AND #$0F
$C0/D679 F0 05 BEQ $05 [$D680]
$C0/D680 BF 85 D6 C0 LDA $C0D685,x[$C0:D685]
$C0/D684 6B RTL
This is how the code reads at the victory dance part for both flawless and non-flawless branch, BUT, for me in battle the characters would not do any victory dance at all and stand still if it was a flawless victory... So in a random attempt to fix it, I tried using the LDA in the non-flawless branch to match the one in the Flawless victory one, and then everything was working. So the LDA in both branches is now reading LDA $C1016B,x
I haven't noticed any problems so far by doing this and all possible victory branches are working correctly (flawless, 1-2-3 characters get hit, all character's get hit, and if Mog is in the party for the not scary enough...) but really I have no idea how that fixed it up and if it's safe...?