Hello everyone. Thank you for sharing your experience. This forum has helped me greatly to get to this point. 

I bought a property that included a d6-5r4xx

I have gotten the pony, and main engine running and confirmed the hydraulics lift. Woohoo

I am running what might be 15+ year old diesel at the moment. Getting a mixed consensus on if these old machines can use old seemingly clean diesel. I have a full tank plus another 60 gallons in drums so I would love to go ahead and use it  

My Question:
All of the control handles feel (with no experience) like they are functioning properly.

I have a dry clutch that I can look at through the floor panel. My clutch handle does not seem to "click". I can push it to about 1" before it hits the front of the slot and I can see the clutch brake pads engaging. BUT the shaft never stops spinning and I can hear the engine bog down as I push harder forward (I believe I read that the clutch should come to a stop allowing change of gears). I can put it into a gear but when I attempt to put it into forward or reverse I grind against gears.

UPDATE I DID GET THE CLUTCH to click backwards and engage. Still no luck with slowing down the disengaged clutch.
But when I pull the clutch backward the 3 spring looking devices do not allow me to click backward. As I understand it that would be a normal running condition with the clutch "lock in" to the flywheel/clutch on the front side.

This does not seem right and I am hoping that I do not break anything

Any advice would be appreciated.

Clutch brake should stop the aft portion of shaft between the flywheel & the transmission, The Clutch Disc assembly seperates this drive train.
With your description of it "bogging down" the main engine when you push the clutch lever forward, the clutch brake is trying to stop the engine.

I suspect you have a stuck clutch plate, either to the flywheel or the pressure plate half, maybe both.
Not being able to engage the clutch could present a secondary issue, maybe someone tried to adjust a worn clutch and with the possible buildup of rust and delaminated disk material, it has swolled beyond limits.

CTS

TY @Ctsnowfigher, As I can see the disengaged rear clutch plate has a nice gap. It would have to be the front plate I assume

UPDATE,
I got the clutch to "click" backward and the lock engaged. Just had to pull much harder than I would have thought.

I am going to publish a video of the un-slowing clutch.

Great idea. I will give that a shot tomorrow to determine if it's truly stuck. I also realized today I have a d6 5r 4xx series. Lucky I have the serviceman, parts and manual books. 

Here is a attempt at recording the issue.

A Parts Book, Servicemen's manual and an Operation and Maintenance Manual specifically made for your Serial Number should be one of the first purchases after buying the machine. Cat uses the S/N to keep track

Starting Engine -
Remember these engines have a very limited cooling system. They depend upon the main engine water pump and tend to heat up if run for extended times.
If you do attempt to move the machine with the starting engine - ensure - compression release is in released postion and fuel to main is OFF. Last thing you want is for the main to fire up. 

***  Another note of caution - those clutches on the starting engines are not large and not meant to take the load of the entire tractor, they are engaged when engine is disconnected from the transmission and compression release is open -  

If you do have a disc stuck, sometimes you can seperate them with a tapered object, much like a screwdriver, driven between the fiber and the metal portions - little at a time in mulitple places around the diameter. Careful you do not overdue as you can damage the components. You want a wide tool - to evenly apply pressure, too narrow and you risk breaking the disc.

Sometimes one can get "lucky" and use both steering frictions (act as clutches which they are) to put machine in gear, with the main clutch disengaged, and machine in a higher gear, best at low rpm on the engine, release the steering frictions in unison while applying both brakes. Just keep in mind if it does not release, you must use the frictions in unison to stop and holding them back, take machine out of gear. This puts a load on the clutch and with it in disengaged position it make break the lining free from the pressure plate/ flywheel.

CTS

My next idear would be point it in a safe direction. start engine and warm it up a bit then stop engine ,put it in third or fourth gear, remember forward / reverse is lever back for forward and push start it with another tractor and drive it around with the clutch disengaged might take a while but it should release.

Thank you all for your advice. I used a prybar to pull the thick 1 inch flywheel (?) away from the rear pressure plate (unsticking it) and greased everything up and it freed up. I have a running functional bulldozer now. Thanks, everyone again.