I'm pretty sure I found the issue after popping valve covers. Lining up camshaft dots by turning the engine, both driver and passenger sides have 2 dots lined up and the crankshaft pulley notch isn't lined up to anything. I posted photos to show what it looks like.
It sounds like with crankshaft pulley notch at zero the drivers side cam needs the 1 dots lined up and passenger side needs 2 dots lined up, is that right? Would I line up the crank to the zero mark and go from there? It looks like I'll need to remove all camshafts and the intake ones are held in by the sprockets that timing belt goes around

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I never did see those compression numbers ;-).... If the timing is off between the valves and the crankshaft we would see bad or no really low compression numbers. The dampener can separate from the internal Crankshaft pulley. If Cylinder 1 is at Top Dead Center, your valve timing should match. Maybe the valves and cams are 180 degrees out to the crankshaft. As unless I am still not awake it takes 2 complete revolutions of the crankshaft to complete a 4 stroke. Perhaps this thread from another forum will help.. :-)

Mechanical Timing Issues 5VZ-FE | Tacoma World

You can go to autozone or most chain stores and get a loaner compression tool to verify your compression is good and the valves are in time with the crankshaft. Then return it.. :-)

Thanks for the info, I realized my last post was kind of confusing. After posting I put the crank pulley at the zero mark with valve covers off. All 4 cam gears are lined up with one dot mark, from what I've read the passenger side should be lined up with 2 dot marks and drivers side with 1. Does this mean the passenger side cams are 180 degrees out like you mentioned? Unless it's more complicated than that

That's how mine was when I was checking my valve clearances a few weeks ago... Get that upper timing cover off and see how everything is lined up.

-Charlie

Dang ok. I did peek behind the timing cover and it was all spot on. If the cam gears all line up using the single dot then it's all in time. I'll move on to a compression test cause it's probably something internal at this point

Amazingly I managed to get it started by swapping two of the connectors coming off the 2 front-most coil packs (not the spark plug wires but the black ones coming from fuel rail area). That was a great feeling but it was immediately running kinda rough and I scanned a cylinder 1 misfire code. Since the motor was professionally rebuilt I'm confident the problem is something else I did.
Smoke was also coming from the passenger side exhaust manifold, where it connects to crosspipe. It hasn't run in 2 years so I was hoping it was something temporary that would burn off, but didn't after 20 mins so I shut it off. If anyone has experience with cylinder 1 misfire let me know

Could be coil packs. Are they new or old? Might be time to replace them.

2 are old so I'll play around with them and see if I can make the code go away.

The main thing concerning me is the smoke, and the fact some smoke was coming out of oil dipstick tube, wouldn't expect that from rebuilt engine. The level on dipstick was really low, barely between 2 dots even though I put in 5.5 qts of 'break-in' oil

Top off the oil, rebuilt engines are what we call completely dry. Move one of the coil packs to #1, if the miss follows, it's the coil pack. It can take a long time to burn off oil from exhaust parts. It could be the gasket soaked in something. Hmmm as smoke coming out of the dipstick tube, is the pvc valve new and not stuck closed?

Also I ment to mention congrats on getting it started!

Thanks a lot man it's been such a project so I'm beyond stoked.

I've put in 6 qts of break in oil total and it's still really low. That seems odd but I can order more just in case. Pcv valve is brand new, I might swap from my other truck just to make sure it's not compromised.
I moved another coil pack to #1 and it's still saying misfire in #1, so something is not adding up still

I swapped different coil packs in and out and tried a new spark plug in #1, still has a misfire there. So based on my reading the next thing would be the fuel injector, or an issue with the ECM somehow

I was just going to say injectors. Most go with the motor west injectors, an I'll replace mine soon too with them.

Enhance Performance and Reliability with 5VZ-FE Fuel Injectors | MotorWest Performance

6-qts is a normal oil change if you use the YZZD3 (longer) oil filter. Add until it is at the full mark. Not nearly all the oil comes out with a normal oil change drain and fill. An extra quart or more would be expected with a new build. Running the engine anywhere between the low and high dots is fine though - that won't be causing any damage.

The dipstick should have an o-ring seal on it - nothing should be coming out there.

-Charlie

What variety of Bot are you, exactly?

You really think its an AI bot? Time will tell. I thought it maybe just a new member. This comment on the thread quite doesn't add up, maybe didn't read the thread properly, or majorly distracted. However, I thought new members had to have so many comments before they can post a thread. If this is a bot, will know soon. :-)