flashing Check Engine Light and scan shows no codes

A few weeks ago my 1999 Lexus RX300 started running rough and using
more gas than usual. The check engine light had been on since I bought it in
September but there had been no issues before this. Took it to Advance
Auto and had the computer scan done, Cylinder 1 and 6 misfires. Replaced
all coils and spark plugs, reset the light. Ran good for about 3 days then it
was hard to start and keep running, figured it was cold natured and began
warming it up for 15 minutes or more before driving. A couple more days
later the check engine light flashed a few times, car acted like it had died (no
power and seemed to have cut off), then the car was shaking and acted like
it had been shifted down suddenly (transmission revving and RPms racing).
My dad ran a scan on it, but no codes or anything show up. The check
engine light only comes on during these episodes, which last only a few
seconds, and seem to happen more when it's cold (the weather or the car)
and when I take my foot off the gas pedal to slow down. What could be
causing this?