By color palettes I mean "From xD0000 to xD1000 is the table of monster palettes, with sixteen bytes for each monster's palette" or something. I'll both take a look at the files you linked to and try out the break point method; if I can't get either one to work, I'll let you know.
(1) Going by Dr. Fail's guide, there are tables for items (0x006C94-0x007017), weapons (0x00639D-0x00659A), armor and accessories (both 0x00659B-0x006C93). All items have an item number, which determines which category it's in (in vanilla 7th saga, anything from 0x00-0x63 is an item, 0x64-0x96 is a weapon, and 0x97-0xFF is armor or accessory). There are a lot of blank spaces, but even using the blank weapon/armor slots isn't quite enough. Fortunately, there's a lot of blank space nearby (xEC75 to xF9FF), so tables should be movable if needed.
You'd also have to show me where to adjust what item numbers are item/weapon/armor/accessory, but Weapon&ArmorSplitPatch.txt from your data shows that you've done that before.
Finally, if I need to cut a couple items to stick with the current maximums, I can; right now my plans have 60 weapons, 47 armors, and 42 accessories, but I can cut back on both if needed.
(2) When an apprentice levels up, vanilla checks their base gain and adds between 0 and 2 (or, more likely, adds between 0 and 1 twice). For example, Wilme (base 4 attack) would gain between 4 and 6 attack, with 5 the most common. I wish to change that a bit:
...Start with the base gain.
...Add between 0 and 15
...Divide by 8, dropping fractions.
For example, suppose Kamil has has a base gain of 18 speed (this may change). It'll add between 0 and 15 (giving a value between 18 and 33) and then dividing by 8 (giving a value between 2.25 and 4.125; after dropping the fraction that gives between 2 to 4, with 3 most likely). The advantage to this is that we can adjust stat gains by 1/8 of a point instead of a whole point (and I'm sure you've seen the gap between fast and slow apprentices!)
(4) If remapping tables doesn't work, I can try adjusting the last two values; if they have no apparent effect, then table remapping should be unnecessary, as we could simply grab a value form the weapon table. I do know that they're 2-byte decimal values and are a bit odd:
* Swords go up from 20 for starter sword to 1400 for SWInsa, then are 0 for all eight post-SWInsa swords (everythign form Barluca to the final boss).
* Axes go from 20 for the starter axe to 2000 for the AXFear, then are 0 for the last three axes.
* Rods/Staffs, claw, and fists are always 0.
* Knives/saber are 140, 200, and 1600.
I'll take a look at them on my own time, as the unusual numbers suggest that they simply may not be used.
And if life needs your attention, I fully understand.