Toyota Repair: Rav4 hesitation/rear O2, timing belt, stumbling

Question
Hi,
My '99 Rav4 2.0 gas 5 speed had been trouble free with 140000 miles, other than a lingering P0401 code for possible EGR insufficient flow. It began developing a slight stumble upon accelleration but was then parked for several weeks for a timing belt & tensioner repair. Now it hesitates badly all the time & also gives a P0141 rear O2 sensor code. I replaced the original spark plugs & checked the resistance on the wires. I have been driving it by gently accelerating & revving a little higher through each gear, to compensate. I can buy the rear O2 for $100+ but did not think that it would cause such symptoms. I would suspect a coil pack or something to do this, sort of like a weak spark. When I first tried forcing the engine, it sputtered badly the whole time & gave me P0300 & P0303 misfire codes. This has me puzzled & reluctant to begin buying expensive potential solutions.

Answer
Hi Greg,
There is nothing more frustrating than intermittent, erratic, stumbling vehicle problems. There are a variety of issues that
can cause this. Don't replace any parts until I know more.
The 02 sensor code is sent because the car is running bad and
the air/fuel mixture is off which makes exhaust gases change.
I've seen way to many parts/sensors replaced over the years and those
parts weren't the problem.
Lets see if I can resolve this. First of all
I need to know as much information as possible. When I look at
a vehicle in person it is much easier to resolve as I can test
drive, listen, and observe. Please tell me in detail the following;

Is it worse when the engine is cold or warm or all the time?
Does it idle rough?
Does it stumble when you first take off from a stop?
Does it die at all when you try to take off from a stop?
It is hard to start?
Is it erratic?
Have you replaced anything else besides plugs?
what was the resistance on the plug wires?
Did you closely inspect the plug wires and boots
for cracks or bite marks from mice?
when a vehicle sets for a while mice like to chew
in wires.
Did a reputable repair shop put the timing belt in?
I've seen cars where the t-belt was installed and
off one tooth and the car runs bad.

Tim