When my idle speed drops below 800rpm, my car gets really lumpy (I'd love it if I had a lumpy cam...but I don't so its gotta be a problem).

I took it to my dad's mate who plugged in some Ford device (into the port above the fuses) and he got an error code saying the ISC cannot control the low idle speed...We upped the idle speed to 900rpm which worked fine when the trans is in P or N (stuck to 900rpm) but when put into any other gear, the idle speed dropped again to 600rpm and the car got lumpy. No matter what we set the ISC speed to, in gear it drops to 600rpm.

Now my dad's mate has worked for Ford for over 30 years doing service and repairs so he really knows his stuff...he told me that this problem was usually attributed to the ECU...which was changed about a year ago because my dad managed to fry the old one (think it was while doin a jump-start but not 100% sure). He also said that because the problem happens while the tranny is in gear, I should get it serviced and flushed (one of the trans cooler pipes was loose and it was leaking alot of fluid) which could also be the problem.

What do you guys think about this problem?

I'd take the ISC off and give it a good clean with carby cleaner or similar, they can get clogged up, it's fairly common.
That'd be my first step anyway, as it's easy and free/cheap.