Correct, cylinder numbering goes from from the serpentine belt to the transaxle (passenger's side to driver's side) from 1 -2 -3 - 4.
Kind of weird that you are getting a weak or no spark - but could explain your misfire codes. Unfortuantly, the ECM signal lines are not easily replaceable - you have to replace nearly the entire wiring harness. But the connections to the coil on plug pack - might be worthwhile to look at them closely and see if they show any signs of corrosion or damage (any cracks in the body connectors).
If swapping the coil packs didn't change anything - I would be looking to check the wiring to each coil on plug unit. The steps of diagnosing these coil packs:
- verify good chassis grounds and power
- make sure the connection is tight to igniter (coil pack)
- verify that 12V+ is getting to the igniter (IGN on, backprobe the connector)
- check resistance of camshaft position sensor
- check resistance of crankshaft position sensor
- check ignition relay
- check ECM signal to igniters
Other possible trouble areas - MAF is dirty or faulty (cause excessively lean or rich injection - may be too much for ignition system) or the ECT sensor is faulty - if reads low, tricks ECM in thinking the engine is still too cold, runs rich until it warms up.
Could be anything from a bad coil pack, bad camshaft/crankshft position sensor, ECM failure, shorted wiring somewhere, ground loops or poor electrical connection. I forgot what pins to test on the coil pack - I've have to look those up later. Same with the ECM - you can backprobe the [ins on the ECM to see if it is generating the signal and providing good voltage to the coil packs. My feeling is it is wiring related - since your getting intermittent results for testing with a spark. Wiring issues are a pain, but not seriously expensive. Hopefully not an ECM issue.
As far as ordering parts - online dealerships, like www.1sttoyotaparts.com is well recieved here (physical dealership - OEM parts). Rockauto is also a good place to check out - stocks both aftermarket and OEM parts - good pricing on components.