I am getting back into D:OS after not touching it for quite a while and one thing that bugged me then is still bugging me - I am red/green color deficient, the map flags are red/brown/something and it makes it hard to seem them against darker areas on the map. Are there any mods/settings/whatnot to change the flags to a color I can more easily see?

On a side:

Why are crafting recipes displayed as books when they are a paragraph long (and not recipes per say, but more of hints on how to do things). I also seem to be daft or something because I get the feeling that some recipes are just flavor (probably doing something wrong). Ex: One of the adventurers guides says to hit a metal shield with a hammer to improve it, so I figured I put a shield on an anvil and use a hammer on it... but nothing happens except for throwing the hammer on top of the shield.

Also, can the initial 'Training Sword' not be improved? I have tried moving it to the whetstone/grinding wheel and the crafting dialogue comes up showing 'Improved Training Sword' as an output but nothing happens. Am I doing something wrong or is it just not improvable?

I want to enjoy the game (I truly enjoyed the original Divinity series [haven't played 2 much though]) but little things keep nagging me (Like: I get the idea behind no map markers for quests, but the quest log is so bereft of information at times I just want to strangle it. Still, I can manage as long as I don't take too long between play sessions)

No, not that I know of.

You need Blacksmithing level 2 in order to drag a metal shield onto an anvil to improve it (you don't explicitly need a hammer). The training sword may be at its limit.