1994 Lexus SC300 2JZ-GE non VVTi

After manual swapping to R154, there has been vibrations from what i thought would be flywheel and clutch. But now i think maybe it is coming from the engine. That it doesnt run right when i give it gas. The vibrations follow the rpm, and it doesn't matter if it's parked in neutral with clutch pressed. And when i drive, it drops rpm when i press the clutch, sometimes the rpm drops so low that it dies. But if it doesn't, it barely goes on at 2-300rpm for a good while, until it slowly start to build up rpm to normal. When i start the car, the rpm is normal. This happens only after i drive.

It was running on 5 sylinders because of bad spark plug. But now i have changed spark plugs and spark plug wires. Looking to change the Distributor cap and Rotor, to see if it changes anything.

But maybe this has anything to do with the fact that i didn't change or do something with the ECU?? I still run the stock automatic ECU. But i didn't think i needed to do anything with it, since it is a 94' that has obd1, and is a non vvti 2jz. ???
I saw something about installing ATEMU, but i thought that was for vvti engines?? Or bypassing the fuel pump ecu??

Or maybe it actually is something not in balance with the flywheel or transmisson.
Specs:
Tripod R154
OEM 1JZ-GTE Flywheel, new (looks to be drilled out spots for balance). (Mounted dowel pins)
ARP Flywheel bolts, torqued to spec and used loctite
Stage 1 1JZ-GTE Clutch Kit from driftmotion
ARP Pressure plate bolts, toqued to spec with loctite
OEM Release Bearing Hub Kit

Any input and tips is appreciated!

I'm not very knowledgeable on the 2jz platform, but maybe cleaning out the ISC Idle speed control valve aka IACV Idle air control valve. In addition check for vacuum lines leaking, damaged or not properly seated.

Small update:
Took down the transmission. Saw nothing wrong, maybe some excessive use of loctite maybe, but not really. Started the car with no transmission, and with flywheel and pressure plate bolted to the engine. No vibrations... So the problem is not in the engine, or the flywheel/pressure plate is not off balance.
So i'm gonna replace the pilot bearing, just because i got a new one. Even though i changed it a couple of months ago. But when i tried to spin the shaft on the transmission, i felt that there was a bit of play there. That i could move it a bit from side to side, while making some noise inside. Can this be the problem??
Yes, the shaft is to be "balanced and centered" when it is going inside the pilot bearing. But still, i might be on to something here...?
The transmission was overhauled and changed bearings by the previous owner, but....

If you've got some noticeable play on the input shaft of that transmission I'd imagine that's a big problem lol. I've never felt any noticeable play while installing a transmission so I can imagine that could definitely be the source of your problems. W58's are relatively simple and if it's something you're not comfortable taking apart most gear/transmission shops should be willing to help diagnose and repair it!

Are there different different input shaft lenghts, or different at all?

Oops, sorry, I realized you've got an R154 - regardless, both are simple manual transmissions and most gear and transmission shops should be able to help you. It might be worth taking it by a shop, having them feel that play in the input shaft, and getting their professional opinion. I don't believe there are different input shaft lengths with R154's, however, don't quote me on that as I'm certainly no expert lol.