Toyota Repair: 99 Rav4 check Engine Light, scantool, trouble code

Question
My 99 Rav 4wd has 157,000 mi, chg oil every 3,000. The check engine came on  solid for a day and went off. That week I noticed it was running  weird, loss of power while driving, sometimes accompanied by a clicking in the engine, but it also happens while idling at a light - it's almost like the engine misses a beat or something but it doesn't actually stall. Took it in, they checked fuled pump, replaced plugs, & the original timing belt (heard it hitting the cover?) but couldn't find why the light had been on. I've had it back a week, same problem! Sometimes it drives like it always did, but other times I have trouble accelerating, never know when, and the engine stutters while driving and at  idle, but now the check engine light comes on when the symptoms occur, and it blinks. Then it goes off within a few minutes. I'm afraid to drive the car. Any hints - how they can they diagnose it if the light won't stay on? Is my car shot already with that mileage?

Answer
Take it back to them and have them see what the trouble code is in the car's on board computer, there is a code logged in the computer which can be retreived with a scantool,if you want to you can let me know what they find and then I can make a recommendation but I do need to know what the code is, try not to drive it too much with the light blinking, you could damage the catalityc converter.