Stan & Dragonof,

Sounds like both of you put the Cardin shaft(s) back together out-of-phase.  To be "in-phase", the yokes at each end of the intermediate shaft must be in the same plane...if out-of-phase, even one spline tooth on the slip joint, the shaft will run rough, tearing up the U-joint needle bearings, the transmission, differential, pinion bearings, etc. 

Swedgemon
GM 90 6/1
Somewhere in Kentucky

A little zinc in the lube oil is usually good (zinc is an anti-wear additive), but zinc in your fuel is not good (leads to galvanic corrosion and varnish deposits).

Regarding injector wear, since last June-July all US refineries have been producing Ultra Low Sulfur Diesel (15 ppm or less Sulfur).  When one extracts some of the longer hydrocarbons and almost all of the sulfur from diesel fuel, most of the lubricity of the fuel is gone.  To overcome this a lubricity additive is injected into diesel fuel as the ULSD is being pumped into fuel tankers.  The alternative to a lubricity additive is the addition of about 2% soy-based biodiesel.  The test standard is a max scar of 520-microns in what is called the HFRR test (High Frequency Reciprocating Rig)...most fuel terminals add enough additive to get a 460-500-micron max scar...addition of 2% biodiesel will give a 320-micron scar.

The real kicker here is that most heating oil is now Ultra Low Sulfur Heating Oil (comes thru the same pipeline and is stored in the same fuel tanks at many fuel terminals)...red dye is added, but NO LUBRICITY ADDITIVE  is put into the heating oil.  When one buys heating oil and burns it in ANY diesel, unseen damage is being done to the injection pump and nozzle(s).  If you are burning 15 ppm sulfur heating oil, be certain to put lubricity additive into the heating oil.  To avoid road taxes when buying diesel fuel, buy Off-Highway Diesel Fuel.  Any fuel sold as diesel fuel will have the lubricity additive (or 2% biodiesel) in it and will run fairly well in any diesel.

Of interest is Caterpillar's stance on biodiesel fuels...any heritage Cat engine (C-series, 3208, 3306, 3406, 3408, 3508, 3600-Series, etc.) is good up to B30 (30% soy-based biodiesel).  If using above B30 (B40, B60, etc.), any fuel related problems are yours.  On heritage Perkins engines (Perkipillars) the biodiesel limit is 5% (B5).  Apparently there are problems with higher percentage biodiesel in engines with rotary fuel injection pumps (Ford, GM, Perkins, Mitsubishi, etc.), although I do not know the precise nature of the problems.

Swedgemon
Somewhere in Kentucky
GM-90  6/1

About 20 years ago in Belvidere, NJ, USA, the Hoffman-LaRoche company installed a stationary Sulzer, smaller, but similar to this one.  It was a 10-cyl, 27,000+ HP unit, turning 120 rpm.  It had a 3-ft bore and 6-ft stroke.  They had serious cylinder-wear problems because the cooling system was part of the plant cooling water system instead of being dedicated to just that engine and they had fuel cleanliness problems for a while until they figured out how to properly run the DeLaval centrifuges that were "cleaning" the #6 fuel oil.  There were 3 huge Brown-Bovari turbochargers (6-foot diameter) up on the top deck and one could stand on a cylinder head and feel the combustion taking place under your feet.  The fuel injection pumps were the size of a Cat D-8K engine and the fuel injector nozzles were about 6" diameter and 30" long.

Probably the most interesting aspect of this engine was torqueing the cylinder head nuts.  The cylinder head was set in place by overhead crane and the cylinder nuts were run down hand-tight.  Then a large spider-looking unit was lowered over the whole cylinder head...over each cylinder stud (with the hand-tight nut in place) was a coupler nut, which was run down over the cylinder stud threads sticking up through the head nut.  When all of the coupler nuts were in place a Port-a-Power hydraulic unit was fired up and hydraulic tension applied to all the cylinder studs simultaneously, stretching the cylinder studs a proper amount.  The head nuts were then run down hand-tight, hydraulic tension on the Port-a-Power was dropped, the coupler nuts unscrewed and the torqueing unit was lifted to the next cylinder...whole process took about 5 minutes.

This engine is gone now, a victim of the NJ DER and bad PR...there was a stack-monitoring unit, hard-wired into the NJ DER in Trenton...the folks in Trenton would look at their meters and if anything looked bad, would write another citation.  Eventually this became a bad PR point with the local folks in Belvidere and H-LaR scrapped the engine.  This engine, combined with a heat-recovery boiler and various other heat-recovery devices, was running at around 90-95 % efficiency. 

I was working for an oil company at the time, suppling lube oil for the crankcase and cylinder oil. To inspect the cylinder walls and look at the piston rings, one would open a hatch on one end of the exhaust manifold and climb inside the manifold with the engine barring controller (to slowly bar the engine over with an electric motor).  If doing a quick inspection (with no cool-down time, as was needed for entering the exhaust manifold), one would open a hatch at the bottom of a cylinder intake box and climb up the intake box (wearing a rain-suit becuase of all the black cylinder oil) to inspect rings and cylinder condition.

Swedgemon
GM-90 6/1

Man without tools is little better than an ape...with no offense to the apes.

If one looks closely at the first of Mike's photos of his governor linkage, in the lower right-hand corner is his gib key puller, setting on the floor...
Swedgemon
GM-90   6/1
Somewhere in Kentucky

The problem with a single U-joint is the vibration mentioned earlier...as power at a constant speed (lets say 600 rpm) is transmitted through a Hooke's joint (U-joint) an angle, the speed on the other side will vary, with two angular accelerations and two angular decelerations per revolution (590 to 610 rpm, in this example).  Now if there is a typical pto shaft (Cardan shaft), with a U-joint on each end, the deflection angle the same at each end and in proper "phase", the speed variations will be damped out and the output will be a constant 600 rpm in the above example.  Being "in phase" means that the yokes at each end of the intermediate shaft are in the same plane...if the yokes are even one spline tooth (at the slip joint) out of phase, heavy vibration, short cap bearing life, etc., will be there to plague you. 
Each Cardan shaft also has a "critical" speed, which is determined by intermediate tube wall thickness, and length of the tube.
Another little often-ignored detail on these devices is that if run straight-through, with no deflection, the cap bearings will Brinnell and fail.

There are at least four types of CV joints...Citroen, Rzeppa, Bendix and a "double-U-Joint".  The Bendix type is seldom seen, unless you have an old Vietnam era duece-and-a-half or 5-ton Army truck (anyone ever replaced a steering axle seal on an Army 2 1/2 ton?).  A Rzeppa joint is usually on the outboard (steering) joint on a modern front-drive auto, with a Citroen joint (3 cam followers and a tulip) inboard, next to the transmission.  A "double-U-joint" is a back-to-back set of U-joints.
I have seen heavy industrial Cardan shaft units run at 1200 rpm, although the cap bearings had short life (about 18 months).  I have also seen a failed Cardan shaft on the back side of a paper machine...talk about a nasty "radius-of-destruction"...
Suggest you seriously look at a Lovejoy (spider-type) coupling if you are using direct drive.
Swedgemon
GM-90   6/1
Somewhere in Kentucky

Hey Geno,
I need your help...check your message box and get back to me.  I would like to get a few photos of a gib key puller posted, but it is beyond my skillset.
Good regards,
Swedgemon

#6 Fuel Oil varies greatly in specific gravity and in how clean or dirty it is...serious filtration is required before going thru a diesel injection system.  Getting rid of the asphaltines (small-to-large lumps of "tar") from the filtration or centrifuge system can be a major landfill problem.  The engine must be started and shut down on #2 FO and the #6 FO must be heated to about 150-180 degree F to get it to flow well and burn correctly.

I'd stick with #2 FO, used hydraulic oil, used ATF, used veg oil, used motor oil, etc.

Swedgemon
GM-90 6/1
Somewhere in Kentucky