I was watching Extreme 4x4 on the weekend, they had a ramjet 350 they were dropping into a toyota, now he said that your fuel injectors need to be angled a certain way or else your idle will be rough. My car has a rough idle when cold, not after being warmed, after warmed up a bit it idles just fine.
I was thinking this may be adding to my rough idle at cold if what he said is true? If it does matter where they are positioned then I do not believe mine are all positioned perfectly.
I know this rough idle when cold is due to a 17 year old dirty throttle body that I have not taken apart and cleaned and a dirty MAF sensor. I have also never checked the TPS
values to make sure they are correct (no digital voltmeter)

Fuel Filter? Check the plugs? Clean the IAC? If the IAC is not seating properly that can very easily cause a rough idle, a lot of people overlook this. Ive seen it clear up and idle a million times. More that Likely if you havnt touched the FIs then they should be seated ok....

Your injectors are aimed by the ports in the LIM/heads and fuel rail combination. They shoudl be aimed fine and have no way for adjustment if you wanted to aim differently.

You have a rough idle w/o doing the standard tune up items. This is completely understandable. Let'* have you do the standard full tune up including removal of the TB and sensors for full cleaning. Not only will your car be lighter form the lack of build up inside the TB.