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Gave it a shot and no luck. Won't even start. Swapped them back fired up.

Can you make a list of everything you changed between when it "pulled really good' and became "super under power"?

Even after going back to the stock jetting, you may need to adjust the air screws to get it tuned will enough to idle and pull away from a stop well.

Got bike with mid range stumble. Once clear of stumble would shoot like rocket. 

Checked valves. 4 where tight. Fixed. Same
Read online about jetting.
got jets I believe they where 110, and 16. Same.
​​​​read more. Got more jets 125, 17, moved clip. Same.
Checked timing. Spot on. Checked points gap. Spot on. 
realized that cold she sounds pretty good but warm sounds bad. Checked coils hot and it went OL. 
swapped coils. Story begins? Haha believe that was everything... also the air screws are all about 1 turn out. I honestly haven't messed with them to much.

Somethings not making sense here. Firstly, jets go up in 2.5 increments, there's no such thing as 16 or 17 size pilot jets. Stock size is 15, next genuine size up is 17.5.
Same with main jets, they go up in 2. 5 increments. 97.5, 100, 102.5 etc. 
What carbs are fitted? Which model of those carbs do you have? 
Stock jets on 650's fitted with vm24ss without accelerator pumps and  without all the smog gumpf  on the head is 15 pilots, 102.5 mains, clip in 4th from top slot, airscrews at approx 1.5 out. 
If your bike has stock airbox and is as above it will run fine set up as above with just minor tuning adjustments then required. Minor tuning adjustments does not include jet changes. 
If your buying jets from ebay, don't, they are mostly cheap rubbish that don't flow at the stated rate and cause more issues than they solve. 

If your issue persists set up as above your issue is not carb related. 
 

You could also try disconnecting the capacitor on the points, this is only there to stop the points "arcing" if it runs ok then replace it. Running it like this for any length of time will burn the points but it will discount the capacitor robbing the coils


 

My apologies I fudged the numbers. This has been a month long project. It was a 17.5, a 102.5, a 112.5, a 110, and a 90 for some reason. I have tried all except the 90. This was all before I discovered the ignition coil going bad. These are all from jets r us. These are the jets I purchased. The ones that where in the carb from when I got it where the 15, 97.5. The carb has a accelerator pump and it is working. At least on a bench test they are all spraying.

what do you suggest I use for a 4into1 with stock air box and accelerator pump?
 

Will do that next and report back thanks.

Sooo I fired her up this morning and let her warm up a little. I then proceeded to turn all air screws to 1.5 turns out. With the choke out she would start up but when I put the choke back in she would die. Messed with the idle a little to see if that would do anything. It did not. I took her for a little spin with the choke about 3/4 out and she did ok just high idle but when I put the choke back in she would try and die out unless I kept flicking the throttle or keeping her pretty open. I got back and turned the screws back to 1 out. She idled fine.

Next I decided to unplug the condenscondensers. Could not get it to idle or run properly. It was acting like it wanted to run but was struggling. I plugged them back in and she fired up and idled. 

One more thing off the list then 
Does it have a vacum operated petcock - if so is it connected ?
Might seem like a random question but are you sure you have "good gas" in it ?

It does not have a vacuum petcock. I also am running it off a gas bottle I have strapped to the bike.

It's the most expensive you can get at the pump. I hope it's good hahahah

This is a most bizarre situation you find yourself in, in my experience this severe lack of power would normally be "fuel starvation" - "massive over fuelling" or the timing a mile out but you seem to have bottomed out all of these 

Choke up is adding fuel. Appears your lean, do you have pumper carbs? Another post found the sensor diaphragm was bad causing drivable issues.