99 4runner sr5 3.4.
The vehicle has been running poorly since the day I have owned it. I just noticed that the timing marks line up with the cams, but not the crank (and it is not 180 out).
My question is; is this an issue where it has jumped teeth?? And if so, what is the proper procedure to time it correctly.

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That is a significant amount off. I wonder if the belt pulley hasn't spun off its keyway or was installed improperly. There is a timing mark on the lower crank toothed gear for t belt also I believe. That would be the ' real' mark to look at for cam/crank timing. That mark you see is for looking at ignition timing. If the cam/crank timing was off that much I doubt it would run at all or so poorly it would be difficult to keep running. I think you are going to have to pull it apart further to verify actual timing.

Here

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Your crank pulley is out of whack but as someone mentioned above, it might not mean that the crank timing gear is. In order to see the crank timing gear though, you'll need to pull the crank pulley. At that point, you should change timing belt and water pump "while you're in there".

From the looks of things, your timing belt is cracking too, so perhaps a timing belt change isn't a bad idea.

Now, the elephant in the room here is, "why is the crank pulley out of whack?"

The crank pulley is "keyed" so if the woodruff key and keyway are as they should be on the crank snout (front of crankshaft), that notch on the crank pulley is indicative of what your crank timing gear is showing... which would mean that some teeth have been jumped.

Another possibility is that the pulley is loose and it stripped out your woodruff key and it's slowly rotated, but your timing is still good (so the mark on the pulley is not in line with the mark on the timing gear. Woodruff keys are replaceable but you have to remove your crank pulley to do it. If the key is trashed and so is the keyway... then you'll need a new crank, but lets not talk about that right now.

Either way, you'll need to pull the crank pulley to figure out why the notch on the crank pulley is so far off.

Interested to see what you find.

Yes, the timing belt does not look good at all. I have thrown so much money at this thing, trying to solve the issue, so I'm not going to replace it until I find out what the issue is.
I will try to get the pulley off tomorrow. I'll keep you posted.

Thanks

as was mentioned by @mckennar you need a belt for sure. The belt pulley is keyed, but usually has a rubber vibration damper so it's possible for it to be off from the crank. That being said Timing off by that far is a miracle the truck runs at all, you will know for sure when the lower cover is off.

This would be an easy fix. Start by turning the crankshaft clockwise until the timing mark on the crank is at zero. Remove the top timing belt cover. Use a spring clamp or c clamp to hold the timing belt to the cam gear at the top so the belt stays in place. Go under the engine and remove the TB tensioner. You will need to reset the tensioner by squeezing it in a bench vice and putting a pin in the hole to keep it closed. If it compresses too easily, replace it. Now go back up top and remove the idler pulley between the cam gears. If you secured the belt to the cams, it wont move on you during the process. Once the idler if out, one at a time, lift the TB off the left cam and rotate the cam so the timing marks line up. Remember this. You want tension on the belt on the right side of the cam. Once you get the cam in place, put the clamp back on. On the passeger side, lift the belt and rotate the cam so the timing mark is lined up. You want belt tension on the right side of the cam, so now replace the idler pulley but dont torque it yet. Now double check the timing marks. In order to get the belt on the right tooth, you may need to rotate the cam gears slightly clockwise 1/8". There will be slack on the passenger side of the passenger cam. Thats what the tensioner does, is take up the slack between the cam and crank. Dont freak out. You will double check the timing now. Reinstall the tensioner but dont pull out the pin yet. The tensioner bolts are 20 lbs ft. With The tensioner installed it will take up some of the slack and keep the belt from jumping teeth. Slowly turn the crankshaft clockwise 2 full revolutions, pausing as you push past the compression resistance and make sure the marks all line up with the crankshaft at 0 TDC. If its on the marks, release the tensioner and torque down the idler pulley. Rotate the crank again 2 full revolutions and make sure nothing shifted. Clamping the belt to the cams is key to this, so the belt dosent go wonky on you with the idler off.

http://s1287.photobucket.com/user/Ka...8d1d4.jpg.html

I was able to strip the engine enough to see the lower timing mark. It has definitely jumped time. I'm going to replace the belt and pulleys. Am I able to just adjust the lower and throw the belt on? Or is there a specific procedure that I need to follow?

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You have coolant leak. That may be causing the belt slippage. It's common procedure to replace the water pump ( which is where the leak is probably coming from) when you replace the timing belt. There are kits with everything you need for around $300.

Right. I picked up an entire kit today. I just need to know if theres a certain way to align everything or can I just line all marks up with the belt off and throw the new one else on

Nope, that's pretty much it. Just line up the marks on the 3 marks on the camshafts pulleys and the crankshaft and spin the crankshaft 2 revolutions and make sure they line up again. There's a lot of info on here about all the other stuff like, moving the AC compressor (or not) to install the belt tensioner (if you have a new one in your kit it's a lot easier)

Highly recommend this tool for compressing the belt tensioner.
I've done it without but wouldn't again.

https://www.amazon.ca/Schley-SCH9730.../dp/B009RXWMNE

I attempted to take the harmonic balancer bolt out tonight, that didnt go very well. I ordered this
Bottom-line pricing on Schley 64400 at ToolTopia.com

Is the tensioner that big of a pain? Its hard to justify spending this much on 2 tools that I may never us again.. I love my 4Runner but this is an expensive maintenance routine..

You can easily compress the timing belt tensioner in a vise.

It is a pain to take off the tensioner though.