99 Lexus rx 300 : Replaced both KS and wiring harness, plugs and battery! P0325 circuit 1 , no overdrive! Why? Could it be a corroded terminal where the harness comes out of the manifold?

Check you wiring harness, sometime the connectors are bad or corroded.

Check engine light on ? What code ? There are many different (DTC'S) - diagnostic trouble codes that can set for knock sensors ! There all don't mean that you replace the sensor .
DTC P0324: Knock Sensor (KS) Module Performance
DTC P0325: Knock Sensor (KS) Circuit Bank 1
DTC P0326: Knock Sensor (KS) Performance
DTC P0327: Knock Sensor (KS) Circuit Low Bank 1
DTC P0328: Knock Sensor (KS) Circuit High Bank 1
DTC P0330: Knock Sensor (KS) Circuit Bank 2
DTC P0332: Knock Sensor (KS) Circuit Low Bank 2
DTC P0333: Knock Sensor (KS) Circuit High Bank 2

The knock sensor (KS) system enables the control module to control the ignition timing for the best possible performance while protecting the engine from potentially damaging levels of detonation. The sensors are located below each cylinder head on the engine block. The KS produces an AC voltage signal that varies depending on the vibration level during engine operation. The control module adjusts the spark timing based on the amplitude and the frequency of the KS signal. The control module receives the KS signal through 2 isolated signal circuits. The control module learns a minimum KS noise level at idle and uses calibrated values for the rest of the RPM range. The control module should monitor a normal KS signal within the noise channel.
Knock Sensor Replacement - Bank 1
Remove the exhaust manifold lower heat shield. Refer to Exhaust Manifold Lower Heat Shield Replacement.
Disconnect the engine wiring harness electrical connector (1) from the bank 1 knock sensor (2).
Loosen the knock sensor bolt and remove the knock sensor.
Knock Sensor Replacement - Bank 2
Disconnect the negative battery cable. Refer to Battery Negative Cable Disconnection and Connection .
Remove the engine oil filter. Refer to Engine Oil and Oil Filter Replacement .
Lower the vehicle.
Disconnect the engine wiring harness electrical connector (2) from the bank 2 knock sensor (3).
Loosen the knock sensor bolt and remove the knock sensor.

code p 0330 refers to knock sensor (KS)2 bank 2 ---circuit malfunction===causes wiring--KS---ECM
it is possible that in changing the harness there is a problem connection or the connection to ks2 is not correct ( not on properly)

Sorry Scott no inertia switch , Two relays , circuit opening relay an the other is Engine main relay if the wiring diagram is correct , hard to tell ! Japanese wiring diagrams ! go to www.bbbind.com free TSB'S an Wiring diagrams .

Possible but unlikely. Code p0330 refers to knock sensor(KS) 2 bank 2-circuit malfunction==causes --wiring --KS--ECM. Replace the KS. The engine light is telling you that there is a problem with sensors in the ECM and that is what will be affecting the performance . Shifting is the area of the TCM( transmission control module ) so have that checked out as well

P0135 comes up, o2 sensor bank 1 sensor 1
P0325 refers to a knock sensor circuit malfunction
P1705 Direct Clutch Speed Circuit Fault

have a tester handy.unplug the light and then turn on the headlights.with tester on 12 volts test plug to see if you have 12 volts. if not the plug is properly corroded or shorted .

I had the same problem with my RX. Had both knock sensors replaced and the problem went away. Be sure to take it to a Tech that has a good scan tool so he can pull the codes and narrow down the problem, From what I understand a constant check engine light is usually not a big deal probably a sensor but a blinking light means major trouble. Take it to a shop that specializes in Toyota and Lexus.

It is an igniter code for one cylinder. Most cars are cylinder 4 but it depends on the engine size. Check each plug wire and see if one is misfiring or not firing. Then you should be able to trace it back to the source.

I'm not a lexus guy , but I'm thinking that you have a vacuum leak somewhere.