I'll just reply in here instead of PM.
I've played a bit through and haven't run into anything that didn't work.  Keep in mind I'm using the version prior to the one you have on Nexus now. 
1.  I'd suggest adding an in-game readme in a file like the "orders" you get in your inventory.  
2.  You should make the logistics and crafting books go into your inventory automatically, you can do it without modifying main by sticking something like this in one of your story files:
IF
CharacterEnteredRegion(CHARACTER_Player1,"Cyseal")
AND
NOT DB_LogisticsStart(1)
THEN
DB_LogisticsStart(1);
ItemToCharacter(ITEM_BOOK_CraftingBook_000,CHARACTER_Player1);
ItemToCharacter(ITEM_BOOK_CraftingBook_001,CHARACTER_Player2);
ItemToCharacter(ITEM_BOOK_LogisticBook_000,CHARACTER_Player1);
Also you can add that readme file to here^.
3.  One of the problems I'm having with the logistics book is forgetting which player is 1 and which player is 2.  Maybe you could set a statement when you start the transfer dialog which has each character say which number they are via CharacterDisplayText.  Or perhaps put a node on the player selection screen which you can press called "Player Identify" which does the same.
4.  For this one "- crafting with external objects - water, oil and ooze barrel, well, oven, anvil - is possible for companions: they will remember your dialog orders, walk to the required object, re-check resources (no exploits) and create the items"
What's the reason the player can't do it?  You can usually make the player do anything a companion can if you use CharacterFreeze.   Is it because the GUI pops up by default when a PC "uses" an external object?  
5.  The editor throws 4 "unable to parse script" errors when loading the mod.  Does it do this for you?