I am going to recheck my timing but I really don't think it is timing related. When I set the valve lash I found TDC marked it on the block at the same time because it did not line up with my tab. Then set the valve lash by what the valves were doing.

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2006 Jeep Commander
2013 Chrysler 200

1964 Valiant 4 Door
1965 Plymouth Barracuda
1967 Chevy Camaro

Not your distributor timing, that's not what we are referring to.
It is the camshaft timing, the relationship between the crankshaft and camshaft. When the timing chain was installed did the machinist degree the cam? If so what did he set it at? If he did like DI suspects and just "lined up the dots", it could be way off. Depending on how far off you may never get the engine running the way you would like.
If your timing tab is indeed that far off for compression at TDC, I'd be looking at it before you go further.
Others here are more adept in describing things, but a good read through posts involving degreeing a cam will give you an idea of what you need to check.

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Mattelderca
78 NYB (gone now), two S series, three old Snow Cruisers and a Doo.

At this point we are referring to the timing of the camshaft in relation to the crankshaft. In other words, the point at which the camshaft is in its 360 degrees of rotation in relation to where the crankshaft is in its 360 degrees of rotation. We are not referring to the timing of when the spark plug fires in relation to the crankshaft position.

To relate this back to your engine, if the engine builder did not "degree the cam" or verify that the camshaft was installed and the timing components (cam and crank gears) were manufactured such that the valves were not opening at the correct time in relation to the crankshaft, then the engine will run poorly because the valves are not opening and closing at the correct time in relation to the piston moving up and down in the cylinder bore. Consider an extreme example. If the camshaft was installed roughly 180 degrees out of phase with the crankshaft then the intake valve would be hanging open at TDC on the compression stroke and the engine simply wouldn't run.

Manufacturing tolerances have become so loose that it is very common for timing components to be anywhere from 4 degrees off up to ten or 15 degrees off. I have even read reports from guys who degreed their cams and found that the cam gear was drilled in such a way that the cam was over 20 degrees out of time from where it should be. A good engine builder or smart person installing their own camshaft will go through the effort to ensure that the camshaft is actually opening and closing the valves when it should be in relation to the crankshaft position.

To check camshaft timing you must pull the vibration dampener, timing chain cover, and valve cover, at a minimum. You will need to use a degree wheel and a dial indicator and first determine where TDC on the crankshaft on the compression stroke is and then calculate at what point the the camshaft events occur. The topic of how to degree a camshaft has been discussed in very good detail elsewhere on the site and on the internet. Do a search o the site and the internet, or wait for DI or Josh Skinner to come along and give you instructions.

EDIT: What Matt said.

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Casually looking for a Clifford hyperpak intake for cheap.

This statement makes me think two things, either the damper has slipped or the camshaft is retarded. If you need to go a significant amount passed indicated TDC to get the valves closed (to set lash) either one of the above has happened.
To find true TDC you could use a piston stop tool in the sparkplug hole.
Then see if indeed the valves are closed.

Edit: We are all hoping that the cam timing is indeed correct.

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Mattelderca
78 NYB (gone now), two S series, three old Snow Cruisers and a Doo.

A piston stop tool would be very beneficial at this point to determine if the vibration damper has slipped and if you are setting the base ignition timing accurately. Do you have a timing tab or has it gone missing? Why did you mark something on the block to measure TDC and how are you determining how many degrees BTDC you are setting the base timing?

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Casually looking for a Clifford hyperpak intake for cheap.

I have a tab but the tab is nearly a quarter turn from where true TDC is. I used a piston stop tool to determine true TDC when I set the valve lash. The reason I marked the block was because TDC was so far from the timing tab.

I just placed a call to my machinist waiting for a call back but let me make sure I understand what I need to know. Did he install the crank and cam and just line the dots up or did he install the crank and cam in relation to the valve opening?

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2006 Jeep Commander
2013 Chrysler 200

1964 Valiant 4 Door
1965 Plymouth Barracuda
1967 Chevy Camaro

To the war room!!!

Sorry I am a bit happy. I think my patience may have been some of the issue. I am idling around 850 RPMs and she is running pretty good. I have a TON of torque but not a lot of the high horsepower. After I drove her around my farm a few times and let her idle on her own she finally settled in and ran great.

Next on the list will be to get that horsepower which I think will come with bringing the valves down a bit.

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2006 Jeep Commander
2013 Chrysler 200

1964 Valiant 4 Door
1965 Plymouth Barracuda
1967 Chevy Camaro

What suddenly changed (found the other vacuum leak?) to get it back in the box...?

How did you utilize the piston stop tool to find TDC? The correct way to do it is to insert the tool into the #1 plug hole, turn the crank all the way one way until it hits the tool, mark a line on the damper next to "0" on the timing tab, turn the crank the opposite direction until it hits the tool going the other way, make another mark on the damper at "0", and then make a mark exactly halfway between the two marks you just made. The middle mark you made is true TDC.

I hope you didn't put the tool in, turn the crank until it stopped moving, and assumed that was TDC. I only suggest it because that sounds like something I would do.

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Casually looking for a Clifford hyperpak intake for cheap.

Honestly I don't know. Like I said I ran it around the farm for about 5 minutes and it was doing okay a little rough but ok. So i decided lets go get some gas and everything clicked in the idle and vacuum stabilized and it all just meshed.

As for the piston stop I did not personally use it a friend did as I turned the engine over.

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2006 Jeep Commander
2013 Chrysler 200

1964 Valiant 4 Door
1965 Plymouth Barracuda
1967 Chevy Camaro

Did you turn it over both ways to mark the TDC point?

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Casually looking for a Clifford hyperpak intake for cheap.

I could not turn the engine both ways because the bolt would loosen but we did turn the engine over twice because I missed it the first time.

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2006 Jeep Commander
2013 Chrysler 200

1964 Valiant 4 Door
1965 Plymouth Barracuda
1967 Chevy Camaro

So are you saying you rotated the crankshaft in one direction only until it stopped and then assumed that that point was TDC?

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Casually looking for a Clifford hyperpak intake for cheap.

No we did turn it in one direction but the cylinder is high enough in the bore to be able to see it. It may not be the best way but it literally took almost everything I had to turn it over in the right direction.

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2006 Jeep Commander
2013 Chrysler 200

1964 Valiant 4 Door
1965 Plymouth Barracuda
1967 Chevy Camaro

I hate to say it, but when you are talking about getting something down to two or three degrees of accuracy, eyeballing it just doesn't cut it.
You pulled all the plugs first, right?

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Casually looking for a Clifford hyperpak intake for cheap.