Yes, Red Line says to use one bottle per tank, so I would use it with 3/4 to a full tank of gas, and not fill up again until you had burned most of it. Once the injectors are clean, PEA is so effective that a very small amount in fuel will keep the injectors clean.
The distributor caps need to be replaced fairly often in the 3VZE, at least as often as the plugs. The crappy aluminum terminals inside the cap get badly corroded and develop a lot of resistance that kills the spark voltage. If the rotor is a Denso, it lasts a little better, but I always replace it with the cap anyway. I would replace these on your motor if they have over 45,000 km on them.
With the miles, starting issues, and rough running, I would add a few things to the list of checks. In no particular order:
ECT - Engine coolant temp sensor. Very important sensor, as it tells the ecu when the motor has achieved operating temp. The ecu will run the motor in "open loop" until the ECT tells it the motor has reached operating temp. In open loop, the ecu ignores O2 sensor input and runs motor on preset mixture and spark timing values. When the ECT says the motor is hot, the ECU switches to "closed loop" mode where it uses input from the O2 sensor and other sensors to calibrate mixture and timing. If the ECT were sending the "hot engine" signal when the motor was cold, the ecu would probably be running it too lean. See the ENGINE - MFI SYSTEM - ECT SENSOR section of the fsm.
Cold start injector - If the motor is hard to start or runs poorly when cold, this could well be the problem. Very easy to test the injector itself with an ohmmeter: there should be 2-4 ohms between the two pins. The test is pretty reliable - if it fails, the injector is definitely bad; if it passes, the injector is usually good.
Cold start injector time switch - even if the injector is working, a bad cold start injector time switch could prevent it from firing. Check the time switch according to specs in the MFI SYSTEM - COLD START INJECTOR TIME SWITCH section.
Compression test - always a good idea in a 3vze. If the compression is no good, there is no sense wasting any money or time on other stuff until the compression issue is addressed. Head gaskets have that nasty habit of blowing, and burnt exhaust valves are not uncommon, either. Compression testers are cheap - just get one that supports 14mm threads, which is a very common size. Instructions in the ENGINE - MECHANICAL - COMPRESSION section. One thing not made clear in the instructions is that you should keep turning over the motor until the gauge needle stops rising.
Coil - Test both circuits with an ohmmeter - specs & instructions in the IGNITION - ON VEHICLE INSPECTION section. This is important since a bad coil will not only make the motor run poorly, but it will also kill the igniter, a very expensive part that otherwise will not usually fail.
Signal rotors & coils - The important crankshaft position and camshaft position signals are generated in the distributor. There are two rotors under the ignition rotor: one with two cams, and the other a starwheel with - I think - 24 lobes. These rotate past three signal coils to generate electrical pulses that the ecu uses to set spark timing and advance. To test them see this post:
Auxiliary Air Valve - should be called your cold idle increase, since that's what it does. It's a coolant-operated, thermostat-like valve that allows extra air to bypass the throttle plate when the motor is cold, increasing idle speed. It is part of the throttle body, below the throttle plate. When hot coolant hits it, the valve closes, reducing the idle speed. It can get gummed up, either blocking the extra air or causing the valve not to close when motor is hot. To test it, screw the idle speed adjusting screw all the way in (the large front-facing screw on the top of the throttle body) when the engine is COLD. The idle speed should decrease, but the motor should still run. Back the screw out to the original position (so you have to count turns on the way in). When the motor is hot, repeat the process. When the screw is all the way in, the motor should stall or nearly stall. If there is no difference in idle speed with the screw all the way in cold and hot, then your aux air valve is not operating properly. Cleaning it may fix it (see below); otherwise you'll need a new throttle body.
Clean the throttle body - pull the air hose off the tb and see if the throttle plate or other parts of the tb are dirty or varnished. If dirty, use an O2 sensor- and catalyst- safe throttle body cleaner, making sure to get the back of the throttle plate and also give the little air passages in front of the base of the throttle plate a few shots with the cleaner. One of those is the "auxiliary air valve" mentioned above. Toothbrush can help as can a clean rag. Be very careful not to get any of the cleaner on the tps, as solvents can kill it. When you're done, check the E, R, & P vacuum ports on top of the tb to verify no vacuum at idle and vacuum at 3500 rpm. See the throttle body section of the fsm.
Check for vacuum leaks - pass an unlit propane torch along the various vacuum hoses, including the power steering vacuum hose and also around the throttle body and plenum seams and listen for an increase in rpm. You can also use starter fluid.
Now all that should keep you busy, lol. Seriously, if you follow all that I'd give you a good chance of nailing down why the motor is not running properly. But if you're still getting codes, post back and more fun suggestions can be yours.