Toyota Repair: RAV4 Check Engine Light, diagnostic fee, scantool

Question
I have a 2001 RAV4 (2WD/5 speed manual) with about 50,000 miles on it -- haven't had any trouble with the car prior to now.  The check engine light recently came on and while it is on, the engine will often jerk or hesitate, most often and noticable during deceleration.  During acceleration, the hesitation is mostly (or completely?) absent.  I took it to mechanic and they recommended replacing the idle speed control motor -- over $400 for parts and labor.  I am a college student and I really can't afford to pay this if it doesn't fix the problem.  I know you don't have a "crystal ball" but does this sound reasonable to you?  The car seems to idle OK while it is out of gear and hasn't stalled.  Sometimes the warning light has gone off and the car runs perfectly -- only to have it come back on.  Thanks for your advice and God bless.

Answer
If it idles ok the idle speed control valve can't be causing this problem and it's malfunction would not trigger a check engine light anyway, I suggest that you find out why the check engine light is on, you can take it to any repair shop and have it diagnosed or I recommend taking it to the toyota dealer and pay the diagnostic fee, another alternative is go by an Autozone parts place, they will let you use the diagnostic scantool  and help you find out what the code is, after that get back to me and I can help you figure this out.