Final, here's one of the manual fixes for Prospecting and Milling. Thanks to hotluck on the forums, I expanded on what they did.

AllowedItemIDs - line 89 - I just added all Legion Ore's and Herbs.

local AllowedItemIDs = {
['109129']='OVERRIDE_MILLABLE', -- WoD herbs
['109128']='OVERRIDE_MILLABLE', -- WoD herbs
['109127']='OVERRIDE_MILLABLE', -- WoD herbs
['109126']='OVERRIDE_MILLABLE', -- WoD herbs
['109125']='OVERRIDE_MILLABLE', -- WoD herbs
['109124']='OVERRIDE_MILLABLE', -- WoD herbs
['124101']='OVERRIDE_MILLABLE', -- aethril
['124102']='OVERRIDE_MILLABLE', -- dreamleaf
['124104']='OVERRIDE_MILLABLE', -- fjarnskaggl
['124103']='OVERRIDE_MILLABLE', -- foxflower
['124105']='OVERRIDE_MILLABLE', -- starlight-rose
['128304']='OVERRIDE_MILLABLE', -- yseralline-seed
['109119']='OVERRIDE_PROSPECTABLE', -- WoD ore
['123918']='OVERRIDE_PROSPECTABLE', -- leystone ore
['123919']='OVERRIDE_PROSPECTABLE', -- felslate ore
}

Prospecting - line 305 - Removed code comments from before BreakStuff_Cache['OVERRIDE...

if(IsSpellKnown(31252)) then
--print("Prospecting")
allowed = true
spellName,_ = GetSpellInfo(31252)
BreakStuff_Cache[ITEM_PROSPECTABLE] = {spellName, 1, 0.33, 0.33}
BreakStuff_Cache['OVERRIDE_PROSPECTABLE'] = {spellName, 1, 0.33, 0.33}
local count = #spellListing + 1;
spellListing[count] = spellName;
end

I believe this fix is in and should be working.

This one is fixed and in, so should be native now, less to change :)