Stock 55mm throttle body should be able to flow around 410 CFM or in the 275HP range.

Yes it had to be contamination in the head that caused all the problems. Big chain reaction. The shims are setup now, I gave myself a heart attack tonight at 1 am all of the shims were out of wack and all over the place like some of them were at zero clearance and others at 15 thousanths of an inch. It took me a couple of mins to realise I had put in all the buckets and shims in the wrong order from 1-8. so they were 8-1. 
 
Check out the difference between the factory airbox and the toms. Sorry for the crap photo.

 

Even better.you should try some e85 too at some point

I would definitely retard the ignition and wait for the tune. Remember the Beams is VVTi.
Just an insight with the knock sensor. The factory unit on all the 3S engines up to GEN4 are single point frequency. That point is what the ECU is looking at. Once you play around with the engine the frequency is changed. Seen it.
 
The best way is with a wide band knock sensor like a wide band O2 sensor you can then home in the frequency where you can see knock. However you cant do this with an OEM ECU. You need aftermarket like i did and even went one step further with a dedicated knock module.
 



But a good substitute is you want to remain on the factory ECU is to use the failsafe knock detector with the wide band knock sensor.
 
wide band
 

i also want the part number, looks like there's multiple wires tho, not singular like the factory gen2/3.

NOTE: If you have a OEM ECU you can not use this!

Ok, Here is something interesting for everyone.

There are a few types of ways to monitor knock, the most common way is with a resonant sensor like installed in all 3S and 5S engines. The other is a Flat type Non-Resonant Knock sensor.

The Resonant type has a few disadvantages: It is only tuned to a certain frequency and it basically "rings" like a bell. Meaning at high enough engine speed it could still be ringing while the next Knock occurs. Thus not letting you know about other smaller knock events in the mean time if they happened.

I guess you could almost compare it like a O2 sensor. Think of the difference as wide band and narrow band.

This sensor is rated around 6khz through 15khz!

For those with a larger bore (thus changing the knock frequency) using a wide range flat type sensor can get you back to actually hearing all your knock.

Anyway.... Toyota now practically only uses a single sensor and that is a flat type made by Denso. They use it on almost all engines even through the Lexus line.

Well, if you have a EMS that can use a Non-Resonant knock sensor you are in luck. Toyota just happens to make an adapter. Simply remove your old knock sensor, screw in the stud, slide the new knock sensor on with the connector facing forward and then bolt it down to 15ft/lbs.

As far as wiring and operation I won't get into that. Please figure it out on your own. I think I've shared enough....

BTW: Incase you wonder what this setup was used on, well... I lied.
The ST246 3S-GTE engine uses this setup. So a 3S engine did use this from the factory.

I test installed one today and it fits wonderfully!

Knock Sensor: 89615-20090
Hex Lobular Stud: 90126-08044
Nut: 90179-08153
Connector: 90980-11875
Repair wire (QTY 2): 82998-12780
The knock sensor is a 2 wire with a braid.
 
NO ITS NOT plug and play. You need aftermarket ECU or the J&S safeguard knock control gizmo.
 
Sorry i have no idea what to retard to . My recommendation is to be patient , wait and let your tuner do it.
 
One thing for sure that i 100% recommend is being able to see knock and letting the ECU control it. One thing is that once the engine is modified there is no guarantee the OEM will do its job right. There are a few to prove this unfortunately :(

Just an insight, the racing Japanese cars that use the 3S block also run 2 knock sensors. They tap a thread in the arrowed part which is exactly the same as the OEM taped part for the knock senor