I'm sorry if this has been done and covered in thread.
Consider taking to Dealer and paying to have diagnostic. Meet with the mechanic as he does job. The masters have seen it all, they can spot stuff we'll miss.
Here a few more thoughts:
When getting codes on specific cylinders I look at all their workings i.e. , spark plugs, coils, fuel injectors & valve gap adjustment. Valve gap issue would be rare but not unheard of. Wires going to injectors & coils must also be tested.
Disconnecting battery for 30 minutes a good idea during any tune up, but normal not associate with specific cylinder codes. I hope that works.
Be careful not to get solvent where axle of butterfly goes into throttle body walls. Cleaner gets into inner workings, some have reported issue after this done.
I use 44k in the gas tank or simular. There are a number of different products that work well to clean fuel system & heads.
Sound is test for valve adjustment, takes a keen ear to hear them. I use a stethoscope. Again Master mechanic knows proper sounds.
I don't recall did you swap coils to see if issue moved! If not do before anything else. You can do same with spark plugs and fuel injectors.
These may not be your issue but worth it anyway:
I'm finding off vehicle fuel injector service a worthwhile endeavor.
When to replace fuel injectors I use FIS in Denver. Inspecting and replacing vacuum lines while waiting on injector to come back is a very nice touch and a must. Look at all ends of lines, replace any that show cracks or have harden when squeezed. Start out with a compression check as you begin disassemble, make sure to inspect each spark plug. I like to line up spark plugs in order they came out. If any coils show signs of heat (running hot) consider replacing.
One more area
@spressomon bought to my attention while working on getting his rig ready for sale
For Sale - 1999 spressoWAGON UZJ100-Series Very Custom Build is the fuel pressure regulator. This is normally associated with varying MPG, again just worthwhile at your mileage.
I don't recall, is your engine a VVti. I'm seeing all (two out of two this year) intake manifold gasket leak on them. As I look through picture of VVti engine, I can see 2 out of 3 leaking. Even if is not a VVti check your gasket. Oil will be coming up side of intake plumes "a capillary action" from gasket, use a mirror to see underside also if going up & down from gasket. It's usually looks like gunk as dust is attracted to oil.
Depending on which engine you have you'll also have some vacuum diaphragm to test. Additionally the VVti has a row of butterfly's running along top inside of intake manifold. Look inside to see if and issue with them.
Once you've totally gone through air and fuel, spark if still present would leave electrical issue.
I don't usually just through parts at problem in hopes. But these things above I'm finding very worthwhile at 150K or more, especially on VVti engine.
If you look through my thread in signature you'll see much of this and how to. Good luck!
