hmmmm...this IS peculiar. To answer your last question...NO, the ecu would not necessarily set a code if the valve timing were to change slightly. The two most likely things that would cause a code to be set would be possibly low manifold vacuum or high or low exhaust temp. These are the only two things that I can think of that MAY be affected by valve timing...however it would take much more than a fraction of a degree to cause a noticable difference in either one. A degree or two of cam timing change in either direction will have DRASTIC effects on the power output of your 3.4L. Did you use a TOYOTA belt or one from autozone? I would recommend using OEM parts especially in these instances. And if you find the timing marks STILL don't quite line up like they should...its always best to err on the retarded side. If you put it back with the cam timing slightly advanced you will notice MORE of a power loss in the normal ranges of operation. Retarded cam timing usualy yields a torque curve at a lower RPM (which best suits normal driving). If I were you, I'd take it apart and do it again. Take your time. Make sure you're checking the timing marks with the 'drive' side of the belt TIGHT. The section of belt (in the direction of rotation) AFTER the idler pulley is the 'drive' side...the section after the first cam that includes the idler is the 'lee' side. It's important to install the belt on the crank and the first cam with the section of belt between the crank and cam TIGHT. With your crank at TDC, take note of the first cam gear's position, THEN make the necessary adjustments on the opposite cam to position it exactly as the other one. Timing belt installation isn't as simple as alot of folks think. I hope I have shed some light on it for you. Its very hard to explain in text. It's really something you have to learn on your own through trial and error OR be shown by someone that's already versed. Good luck!

P.S. On another note...be very careful NOT to get it too tight. Alot of folks get their timing belts too tight. This will invariably cause it fail prematurely. I always get the belt installed using the procedure mentioned above, then I use a wrench to turn the engine in the normal direction of rotation which takes up ALL the slack on the drive side of the belt. Then I note the natural tension on the drive side and make the necessary adjustment to the idler to set the tension on the rest of the belt to match that of the natural tension that ocurrs on the drive side. LOL...hope this all makes sense.