Fallout 3 GOTY + DLC Pure Ninja Build?  

Ok for skills:
sneak-cause as you know ninjas sneak etc.
melee weapons-this will help shishkebab.

Try put your primary attack skill like melee weapons up the most then have sneak 2nd and something like lockpick or science 3rd.Make sure not to spread the points across all the skills,pick your favorites and stick to them.

For Special:
Perception-will help show enemies are so you cant sneak up and kill them.
Strength-will help how much you carry and your melee weapons.
Intelligence-wont have much to do with ninjas but it gives you more skill points each time you level up so you can help your ninja skills.lol.

Make sure to tag good skills also.

As for the shishkebab:
Locations:at level 26 I think (have to have broken steel) you can get a perk called warmonger (I dont know how to spell)that will give you the schematics for all custom weapons(level 3 versions).You might need high intelligence.

Perks:
If you want a ninja character get perks like light step etc.Just get whatever helps your character.

Good vs evil:
If its your first playthrough do good so you can get a feel of the game then on your 2nd playthrough have some fun and do bad.

Well there is a ninja perk that allows you to do paralyzing punches when you are unarmed. Other then that just make his sneak really good and stuff like that and it should be an awesome character.