So i’ve been working on this issue for a long time. It seems like my car is misfiring although i’m not certain. At idle at operating temp my rpm’s in park and neutral are ~800, in reverse or drive they are ~500. When i come to a stop the car starts shaking and the rpm’s bounce down and up 450-550 slowly. My car also starts backfiring while this happens. After that when i start driving if i give gas it will backfire a lot then smooth out as i speed up.
Sitting idle in drive every time i hear my car backfire the engine shakes a bit and i hear some sort of clicking noise (relay maybe)

I had a cel that recommended a new throttle body so i got a new assembly
after that i got a cel that recommended a new vss so i replaced both.
now i have no cel but the issue is still here.

My previous attempts to fix this have involved cleaning my tb, fixing vacuum leaks, removing cats, new spark plugs (haven’t done wires or coils), new transmission, and new throttle body.
let me know of any recommendations

I would also like to verify all my vacuum lines are hooked up to the right spots if anyone has the same engine and can send a picture. The guy i bought this from had replaced the engine and it was missing a lot of components in the engine and came with multiple important lines capped off.

lastly my specs are a 2000 lexus sc300, 2jzge vvti, and a340e transmission

 

If I were you I would check for a sticking injector or a cylinder that is flooding out. Remove the plugs and check for any specific plug being black and covered in soot or visibly wet if the plugs are removed shortly after running the engine.
To isolate a misfire you would get the car to operating temp idle and briefly disconnect each coil pack then listen and feel the engine for any change in operation. If the engine noticeably bogs down that cylinder is contributing to the firing order, but if the engine does not change that cylinder is not firing.
If not done already spray off the intake's various crevices and such with brake cleaner and listen to hear if the idle speed changes. This would indicate a vacuum leak, which can be the cause of a low/erratic idle.
Finally, the ECU has to learn it's idle. If not performed previously and the throttle assembly was replaced, it may be worth unhooking the battery so that the engine computer can re-learn proper idle parameters. I don't know the procedure off hand but typically you'll unhook the battery negative terminal for a while, hook it back up, then let the car warm up to operating temp with the A/C off and all electrical loads disabled.

Good luck.

 

Thanks for the recommendations, tomorrow ill pull my plugs and figure out if one of my cylinders is having issues. I'm going to buy a full set of injectors from lexus tomorrow as well.

Earlier today i hooked up my smoke machine to check for leaks and found a big leak on a hose that was ripped, that somewhat helped the rough idle.
After I fixed the leak I unplugged my negative terminal for 15 minutes and turned my headlights on to drain the rest of the charged power which i believe resets the ecu.
After driving for about 45 minutes today the cel is still not on, the car is driving better and smoother but it still has that slight backfiring and a little bit of bucking.
Since buying the car I haven't messed with the fuel delivery system at all, I might just take out a decent amount of money and buy a new fuel rail, filter, and pump, along with the new injectors

 

So today i went to pull my spark plugs to check their condition. At first i had my car idling in drive to let it warm up, and i noticed my middle coil pack was arcing onto my engine. Previously i had mentioned a clicking noise that i had suspected to be a relay but it turned out to be the electricity making that noise every time it arced. After closer inspection the connector clip was completely gone! The connecting wires were directly plugged into the coil pack with no clip supporting them. I unplugged my battery and took the coil pack and the spark plug under it out (pic below) and I bought a new clip at autozone and got the coil pack wired up correctly.
I plugged the battery back in and started the car and it started up amazing, my idle was sitting higher around 800 in drive as opposed to before at around 500, but right when i pulled off i heard my engine start to misfire worse than before i replaced the connector. as i accelerated it went away. I drove around for about 10 minutes and pulled into a parking lot to sit there so i could see if it was idling as poor as before. After sitting in d for about 1 minute the rpms slowly dropped back down from 800 to 500 over the next minute and i heard the engine misfiring. The bogging is fixed (every time the connector would arc my engine would bog) but the misfire is now worse. After that i drove back home and was waiting for a cel but none popped up yet, i drove for a total of 30 minutes.
I bought an infrared temp reader today and tested my exhaust temps and it seems like cylinders 1 and 6 are 20 degrees celsius colder than the rest.
I ordered a set of new spark plug wires from ngk, a set of new denso fuel injectors, and in a minute here i’m going to order 3 new coil packs. If anyone can help me diagnose this further i’m all ears

 

Verify the new connector was installed correctly. In addition verify the rest of the coil pack connectors are sound as well. Clearly someone's been less than careful around the wiring and you should go over any connectors to make sure they're still good.
Also, if not done already I would check all engine grounding points. Have seen weird idle and performance issues stem from improper engine grounds (rust or just left loose) You mentioned there has been extensive work done to the car and there is at least one ground down below where the transmission is.
Try to rule stuff out before bouncing around all over the place. Remember, engines need Air, Fuel, Spark and Compression to run. If you can rule out any category definitively you are one step closer to finding the weak link in the combination. Given you've found a clue in the ignition system I would ensure spark is 100% before continuing further.

 

it’s late so i won’t have time to check the other coil packs or anything, i’ll take a look tomorrow. i should note the first coil pack has a connector but the connecting clip is cracked so it slides on and off without pushing the tab, do you think it’s worth replacing? or is there a good way you know of to test if the connection is strong enough to keep it like that.

 

It's your call, a lot of the connectors on my car have lost their retaining tab but still hold when clipped into pins. If it takes enough resistance to physically pull it off the coil pack and the rubber seal is holding up it's fine.

 

Okay so i think this issue is narrowed down to a fuel or ecu issue. I have verified with a smoke machine that i have no vacuum leaks, replaced my maf, and bought a new throttle body assembly. Air doesn’t seem like the issue here unless there are some vacuum lines hooked up incorrectly. For sparks i replaced my spark plugs, coil packs, coil pack connectors, and ignition wires. If im correct thats everything i need to replace for spark. I guess my next steps will be replacing my fuel injectors when they deliver then replace my fuel filter. Hopefully i won’t need a fuel pump because those run a couple hundred bucks but if i need i’ll replace it. Lastly I have heard of ecu capacitors causing random issues. I think if the fuel injectors and filter don’t fix it i’ll start on replacing all my ecu capacitors.
Earlier tfwnoturbo mentioned checking my grounds, I still havent had a chance to check them all. I double checked the ground under the transmission is set up correctly.
At this point my car is not having issues with shaking or backfiring, it runs good when i start the car and drive until i come to a stop. When I stop the car it is fine until it sits for about 1 minute and the car will misfire/jerk then the rpms will slowly drop and the car starts to run rough. (Misfires while I drive off and runs rough at low speeds until shut off and started again)
Something to note is in the past I have gotten multiple random engine codes that im not positive were accurate. One of them was a code for a leaking gas cap, i verified my cap was fine. I also recently got a vss code, I did recently replace my transmission which had new vss sensors on it but after replacing them with my old ones nothing changed but the cel went away. Maybe this points to an ecu issue?

 

Don't quote me on this but 98+ stopped having capacitor issues, they use revised caps. Not impossible but highly improbable. My first SC was a 2000 model year and had no running issues other than a VVTI OCV failure at 170k or so.

 

what kind of issues did you experience with the ocv failure? And if the 2000 sc300s come with upgraded capacitors i’ll wait until i’ve replaced everything fuel, compression and timing related. I put my new coil packs on today and they still didn’t fix my issue. At this point my car sits at 500 rpms in park and 350 in drive right after it heats up. At idle it sounds choppy and at low speeds you can hear the engine miss, i’m not getting good engine power either