I finally got the fuel filter on my D6 5R. The fuel injector has been cleaned and ready to be timed when I put the governor on. In hindsight, I'm thinking I should have turned the engine over until #1 cylinder was on TDC aligned with the flywheel timing mark THEN put the fuel filter, injector and governor on. At least 3 of the cylinders would be ready to set on the injector. It looks like the timing marks are going to be REALLY hard to see with this stuff bolted on as it's just under the fuel filter. The blade cylinder and support bracket are right in the way of looking into the inspection cover for timing.  Does anyone have a trick, method or solution for this? Thanks.

Hello unstyled
I can't decipher what you are asking here. I can't think what timing marks are in an access panel under the filters. As far as I know the timing marks are the standard flywheel for TDC and timing gears for gear alignment and the rack and individual pump gears. The injector pump cam shaft has an off center tongue and groove coupling that can't be installed out of timing. Are you talking about the inspection cover that covers the rack?
What do you mean "The fuel injector has been cleaned and ready to be timed?

The fuel filter, fuel injection pump and governor were all off and in a box when I purchased it. Everything has been cleaned spotless and ready to install. Yes, I am referring to the timing/inspection cover with the timing marks on the flywheel that are directly under the mounted fuel filter I put back on. Next is the injector pump and governor to be installed. Matching the timing marks to set the fuel pump distance of 1.736 inches looks to be difficult as it's very hard to see the timing marks with all the stuff in the way.  Not sure how I can look to see where/when the timing marks match up on the flywheel inspection cover. It's going to be hard to visually see with everything in the way. Hopefully this info helps, let me know if you need more info. Thanks PhilC

Ok I think there is a possibility that you are misnaming the flywheel as the access cover for it is on the bell housing at the rear of the engine on the right hand side near the sump fill cap/breather. Nowhere near the fuel filter tower.
Was the accessory drive shaft removed from the timing train? If only the fuel filter and injector pump were removed then it should not have been disturbed as you need to remove the timing cover to get it out and that is a major undertaking. The accessory shaft drives three items, the injector pump, fuel transfer pump and hour meter. The injector pump cannot be mistimed in relation to the accessory drive shaft and the other two don't need to be timed.
The 1.736 (1.734 in my manual) is the height of the pump lifters and the procedure you are following is to set the height based on a set piston being at top dead center on compression stroke which can be confined by looking through the aforementioned flywheel access cover where you will find a pointer and most likely numbers on the flywheel that are difficult to read. These marks will tell you when the piston is at TDC but will not tell you if it is on compression stroke. To find that out remove the valve cover and observe the valves on number one piston. They should be both closed (rocker arms should be loose) when the pointer in the access cover is pointing to number one piston TDC. Firing order for these is 1-5-3-6-2-4. So you would set number one turn the engine over 120 degrees and set number 5 and so on. There is a short cut for adjusting valve clearance but I would not shortcut the adjustment of the lifters.

You are so right PhilC, I just now went out and saw the flywheel timing cover on the rear right side. There is a small cover right under the fuel filter on the front left side and I thought this was how #1 cylinder was determined to be on TDC. Wrong! This is going to be much easier than I was anticipating with easy access to timing. Ha! The accessory shaft is attached, I now understand how the fuel injector pump cannot be mistimed/set provided the engine is in the proper position. Thanks for pointing out all of my errors, I'm so relieved. 
 I've got other issues to address as I get to them, stuck engine clutch ( not steering clutch), a shot pony motor, broken leaf spring ( I located one from a member of this forum) a few other smaller issues - I hope - and the usual unknown. One step at a time. Thanks again for the reply and instructions.

Hello unstyled
It is my pleasure to help you out with this. I have three of them myself and have spent considerable time over the years working on them.

I cannot understand why the previous owner removed the fuel filter tower unless there was a blockage or something. Did you check all passages are clear before putting it back on? Also there is a lip type oil seal on the accessory shaft in the tower.

The machine ran rough from what the seller said. He attempted to clean the fuel filter and probably injector pump hoping that would take care of it. I guess it still ran rough afterwards so he had the injectors rebuilt then gave up working on it. The dozer was a couple hundred yards away from the shop in the woods making it difficult going back and forth for tools, etc. He's 80 years old so I can see that. I am very meticulous about cleaning important parts like these so I'm not too worried about that aspect. When I feel like I've correctly timed the injector pump the next obstacle is addressing the pony motor. To be continued. Thanks PhilC, I appreciate your help.