I find it very rewarding to discover everything on your own. If you follow these tips you shouldn't miss anything in the game.
1) You don't need to draw maps, cartographer is more than enough
2) When exploring areas, make sure you turn in ALL four directions in each tile especially when mapping out outdoor areas. This is important because some clues and even some dungeon entrances will only be announced to you when you are facing in 1 direction. I reiterate, it is very easy to pass up a dungeon entrance or clue by not following this rule of thumb.
3) Write down EVERY clue you come across no matter how insignificant it may seem. From fountains to things you can eat even.
4) Make your own clue book in a notebook or use a file on your desktop. Try to organize your clues wisely so it won't be confusing. Have a section titled "Points of interest" for both outdoor areas(C1,D2 etc.) and towns. Make sure you subcategorize the outdoor letter-number locations and tows. You should list everything from dungeon entrances to tough battles you can't do yet. Seperate other clues found into categories like, "Castle Clues" Spell Clues" "Hireling Clues" "Miscellaneous Clues". This is much less confusing then having sections like "Dungeon under Sandsobar Clues" .
5) If you choose to not use the clue book you will find stat adding locations much later in the game then you would like to. The only stat that really is important for finding the earliest is stamina. Finding the stamina adding locations may feel bad when you are like lvl 10. Don't worry though you can always make new characters if you so wish, or wait till you find +HP oppurtunities in the game. No big deal.
It is VERY rewarding to beat the game by yourself. So give it a shot. Good luck and have fun.

Wow. Playing MM2 sounds like a school project!

I have a walk through which I try not to use very much. I also downloaded the stats for weapons, armor, etc and put in a notebook. I admit I do use that often. I write down all the clues. I do this because I don't want to spend too much time with this one. Kinda want to move on to Balder' Gate or Fallout next. I am enjoying it though, and even with help this is going to take a while with the massive levels of this game.

Identifying items was the one thing that made me use the cluebook. I didn't mind drawing maps, but laboriously identifying every item was quite annoying. I minimized spoilers by searching the PDF for a specific item after I found it.

Same here... I wish there was some in-game method of doing it...

You can ID items at any blacksmith's shop. There might be a spell to do it, too -- I can't remember (I remember an ID monster spell... hmmm).

Anyway, use the manual. :-)