Apparently the website is gone. Unfortunate because it was about the best one I've seen for showing how to repair the damage.
I searched around on the web, it was the only one I could find that showed the repair. Google does have snapshot of the page but the pictures are gone.
I'm going to paste it here so it's preserved as Google probably won't keep it around for long.
Even without pictures this gives a good idea of what's involved, it's lot of work, at least 8 hours for an experienced mechanic.

Dowel Pin Repair on a Cummins B series 5.9 liter.

Several people on the TDR website showed interest in learning more about the work involved in replacing a broken timing gear housing from damage caused by the upper dowel pin working its way loose.

You first remove the bumper, fan, radiator and loosen the A/C condenser. It is possible to remove the intercooler without breaking the A/C lines and losing the charge of freon as shown below. You must be very careful though. The harmonic balancer and electrical sensor are being removed here.



The picture below shows the timing cover with the idler pulley removed. The crack caused by the dowel pin is always under the idler pulley and cannot be seen until it is removed.



This crack is the first sign of the internal damage.



You then remove the case cover and expose the internal timing gears. This is a good time to rotate the engine until the timing marks on the camshaft and crankshaft gears line up. You can see by the 'V' mark on the camshaft gear that this engine needs to be rotated almost a full 360° to align with the white mark on the crankshaft gear at the two o'clock position.



With the cover removed you can see more of the damage caused by the dowel pin. On this particular engine, no visible damage was done to the timing gears.



Now the easy part is over with. Removing the timing housing is a bit more involved. The vacuum and power steering pump assembly can be removed with two bolts. The vacuum pump gear does not need to be removed, it slides out through the back of the housing. Four nuts that hold the injection pump to the timing housing must now be removed. The two outside nuts are easy to access, but the inner two are difficult. Below is a picture of the inner two nuts. A severely bent hand wrench will access the top nut. The bottom nut requires more imagination.



The next step is to remove the camshaft. This requires removing all six valve covers, rocker assemblies and push rods. There obviously isn't room to extract the pushrods from the #5 and #6 cylinders. Dodge has conveniently left two holes in the cowl of the truck just for this purpose. The holes are filled with two rubber plugs. To gain access to these plugs, the windshield wipers and plastic cowl must be removed.

You will need twelve 1/2" dowel rods cut one foot long for the next procedure. Each rod needs to be tapered down to a sharp point. Begin the taper 1" from the end of the rod. Now cut a 1" slit in that taper. You then drive the dowel rod into the tappets and pick them up off the camshaft. A rubber band will hold the dowel rods up and keep them from falling back down. It's very important for the dowel rods to be secured to the tappets firmly. The camshaft is likely to hit the tappets while being removed and reinstalled. If one of the tappets falls off the dowel rod, you will need to remove the oil pan to get it out!



Now you can remove the camshaft. It will take a steady hand to slide it out. Be gentle. When the camshaft is positioned correctly it slides out easily.



Now the timing housing can FINALLY be removed. Now you just need to clean off the old gasket and reassemble.



The four studs that mount to the injection pump as well as the timing pin need to be moved from the old housing to the new housing as shown below.



This photo was taken from the back side of the new case. You can see that the hole for the dowel pin is now necked down so the pin can no longer work its way out. Too bad this wasn't included in the original design.



We used a magnet to retrieve the dowel pin out of the oil pan before reassembly. It looks as if the pin was ground on for quite a while by some of the gear. Notice the blue marks from heat!



Now you reassemble in the reverse order. Make sure you install the intercooler BEFORE the radiator. Isn't that right Cord?



This final picture was taken of the bed of Cord's truck after the job was complete. We didn't realize just how many tools the job required until we saw this.



I hope this helps some of you understand the work involved in replacing the timing housing. This was meant as a general overview and not a set of step by step instructions.

 

The balancer and fan are the EASY part! You have to remove the entire timing cover which entails removing the camshaft. I wouldn't think 1/2 qt./wk. would have any effect on the valves. I would suspect the pin is possibly rubbing against something causing the extra noise or did damage to the gears when it let go. IMHO you NEED to take (get this taken) apart before you drive it much longer. It seems $1300 is about the labor, the case is about $300 plus whatever else you did. I'm betting you gonna chew the hell out of a $2000 bill by the time you're done.

 

That link is dead. Doesn't exist anymore. Looked like it was informative as the same link comes up under dieselstop and TDR multiple times on a search.

 

Try this
KDP REPAIR

EDIT: Well, I just loaded the page a second ago... but it won't now.

 

Worked for me so I cashed it at google in case it disappears again

http://72.14.203.104/search?sourceid...2Fdowelpin.htm

 

I printed it out just in case. My next question is, what year truck is this done on and how much difference is there between the 12V and 24V repairs in this area?

 

As I understand, it is mostly a 2nd gen 12V problem. The weight and harmonics of the P7100 vibrate the pin loose. It is not unheard of for it to happen to an early 24V. Cummins made a running fix around 2001 in the timing case so there is no definitive date where you are safe.