Stumped by random misfire

[aranlar]

2003 base FWD 162k miles.

I bought this vibe a month ago. Ran fine, a little underpowered and some exhaust noise.
Started getting p0300 and p0301 p0302 p0303 p0304 and p0420 after couple days driving, can feel slight misfires at idle, sometimes a slight hesitation on initial acceleration
Took care of exhaust leak, shop put in a spacer and new donut gasket and that took care of loud exhaust but still get p0420 along with the misfire codes.
***Each time I've fixed / tried anything I have reset by disconnecting battery negative terminal for 20 mins.
First thing I did was replace plugs with the NGK laser iridiums - No change in symptoms.
Noticed intake manifold gasket was the black one, replaced it with orange from Toyota - no change.
Cleaned MAF twice - no change
Replaced air filter.
Replaced PCV - no change
Ran Techron thru a few tankfuls - no change
Checked battery and alternator at AutoZone, both test good. Cleaned battery terminals and replaced cruddy looking positive terminal.
Checked ground points with resistance setting on multimeter all read 0 ohms to ground at battery.
Pulled and inspected injectors, put back in with new O rings - no change.
If I pull any coil or injector connector while running idle gets worse so it's not any one cylinder that's causing it ???
Checked vacuum with gauge and all reads normal from what I can tell.
Pulled crankshaft position sensor and cleaned , didn't know how to test?
Pulled OCV valve (it looks new from prev owner) it had oil on it so it's good?

Tried to pull VVT-I filter but too tight without taking intake back off to get some room but it's hardly that causing misfires???
I know injectors could possibly be clogged, coils could be bad but can't really afford to just throw parts at it to try and fix it. I have a OBD scan tool ordered in the mail and will be able to get into more in depth analysis like fuel trims etc once I have that.

I have searched and searched all over internet for answers/ideas and having tried the more obvious stuff I'm pretty stumped on this but need to troubleshoot some more as I can't really afford to just drop it at a shop right now.
Any pointers from anyone??? I need to pass inspection to get registered etc

[thebarber]

P0420 is a bad catylitic converter

If some has broken away blacking the exhaust it'd explain your lack of power

[thebarber]

get a new intake manifold gasket as they revised the design for the 2005 and up model years, iirc.

[aranlar]

From what I understand P0420 is not neccesarily just a bad cat that needs replaced. The P0420 could just be getting thrown by excessive gas from misfires. I've ran a vac gauge test that does not indicate exhaust blockage. Again... I need to troubleshoot and pin it down rather than just throw parts at it.

[aranlar]

Already replaced intake manifold gasket with newer orange one from Toyota dealer.

[circuitsmith]

How do the fuel trim #s look? Over 5% is suspect.
Do a compression test.

[aranlar]

Waiting on delivery of obd scan tool to check out fuel trims. Have not done compression test (never done one before) but I know I can rent a tester and to do it soon.

[aranlar]

Also, CEL has never flashed , just comes on and stays on. Car drives around and accelerates just fine . Just notice a slight miss sitting at lights but never feels like it's gonna die. And just one small slight hesitation on initial acceleration sometimes.

[aranlar]

Soooo... Update!!! A week ago I took off and throughly cleaned throttle body and IAC valve, replaced mounting gaskets for both and that seems to have taken care of misfires. Had a couple of "pending" misfires show up on scan tool since but they cleared themselves quickly without ever throwing a full code and lighting check engine light. Still have a P0420 to clear and tried both the resistor and diode mods on output wire of downstream o2 sensor. Neither worked so I was doing antifouler trick on downstream o2 today, sensor looked very cruddy so decided to get new one anyway. Decided to pull upstream o2 just to have a look and found... OMFG someone had installed a non fouler spacer on the upstream o2 !!!! That's a big no-no!! Upstream is used to control air/fuel mixture. I can only assume previous owner was trying to clear the p0420 and worked on the wrong o2 sensor. I went ahead and spent the money on a new upstream o2 coz at this point I want to be sure everything is good. I have yet to take it thru a drive cycle, gonna take her out for a good long drive tonight, but am pretty sure this is gonna be an end to all check engine codes for now and I'll get it thru emissions inspection in couple of days.