Some instructions I posted on the ATOG users group, but useful for anyone with a QSB5.9. First try took nearly 6 hours, second one about 3, I'd be surprised if anyone can do a good job of it in less than about 2.5. No special tools or skills required, but not something I'd choose to do rolling around in a seaway.
1) Flush engine raw water system with fresh - not strictly necessary but results in all your spills being fresh water rather than salt. Place absorbent under area to catch water and diesel spillage.
2) Drain aftercooler from lower pencil zinc port. About 1 gallon will come out. (You did shut off the seacock, right?)
3) Depower engine at CAM Breaker, on my boat this was located in the tank room at the forward bulkhead. Loosen the screws and pull out what looks like a very large spade fuse. The Engine switch will not depower the ECM, only the starter motor.
4) Remove the fuel cooler by loosening hose clamps at the raw pump and aftercooler, this can be laid down out of the way without removing the fuel hoses.
5) Remove the afterooler - this looks like it just *might* be unnecessary, and I tried for a long time to not do it, but it is actually necessary. Loosen the hose clamps at the air inlet and outlet, and the water outlet at the top. The air inlet connects to a tube to the turbo, it is easier to take off and reinstall if you loose the hose clamp at the turbo, pull that off, then pull it off from the aftercooler. The water hose can be pulled loose without difficulty. The air outlet connects to the intake manifold, and the aftercooler is best pulled out of this as it is removed since there is no flexibility at that end. I found the easiest way to remove it was to remove the 12 pt bolt holding the forward bracket to the block (which also secures the fuel pump wire, 10mm wrench), then loosen the two large bolts aft and underneath with a 15 mm wrench. Then reaching around behind the top remaining bracket, remove the hidden bolts with a 13mm wrench and some swearing. This bracket is fastened with two readily visible bolts on top, one of which is diabolically blocked from removal by the #5 injector pipe. Once the hidden bolts are backed off a little I could reach them by hand and spin them out, jiggling the aftercooler a bit to unload them. With those out, remove one of the larger bolts on the bottom bracket and screw it into a second set of holes just below on the bell housing. This allows the aftercooler to rest on that while you wrestle with it. Unscrew the remaining bolt and supporting the weight, remove the aftercooler (about 35 lbs maybe?) and set aside on the carpet you prepared to receive it. If it has not been removed recently, getting the hoses unstuck with a tool of some kind first will make it much easier. The best tool for this I have found is a cotter key remover, also sometimes known as a windshield installation tool and occasionally even as a hose remover.
6) Remove power leads to ECM using a 7/16 wrench. Be vary careful, Cummins in their wisdom has applied some kind of hard black substance which makes the nuts difficult to turn, and to my surprise the studs are soft brass and twist off with ease requiring another repair!
6) Unplug the three large connectors with a 4mm allen key, unscrewing this automatically ejects the connector. There is another smaller one with a locking tab as well. Remove the three nuts securing the bottom of the ECM cooling plate (13 mm wrench), this will release the Jubilee clips holding the wiring harness and allow it to drop down out of the way.
7) Remove the three nuts securing the SIM module (10 mm wrench) and the washers behind them. The electrical plug for this has a securing tab, which itself is secured by another plastic safety. Pull the SIM module off and find the bolt securing a grounding strap underneath (10 mm 12 pt wrench). It might be possible to remove the grounding strap from the block end, not clear that is any easier.
8) Remove the top bolt securing the ECM plate, there is a spacer behind the plate which will drop as you remove the bolt unless you catch it.
9) Undo the fuel hose to the upper aft corner of the ECM cooling plenum, this requires a 7/8 open end or largish Crescent wrench. The connection is a face sealing o-ring and should not be terribly tight. Expect a small amount of diesel spillage. It may be possible to get to the pump without removing this, but it certainly makes it easier to undo it. See that the o-ring remains in place on the plenum fitting face groove for reassembly.
10) Wiggle the ECM plate free of the lower three studs, pull it down and under the hard high pressure fuel line going to the common rail, then pull out a little and hinge to port and forward like opening a book. The remaining lines should flex enough to gain access, and now the pump is finally visible! I was able to tie the plate off to the ladder through the top mounting hole to work on it, resting the bottom on the engine stringer.
11) There are four small bolts securing the fuel pump clamps. Loosen them all, and remove the top ones and flip the clamps down. The inlet and outlet are banjo fittings requiring a 17 mm wrench. The pump has an obvious small hex on its body, but this is useless for loosening the banjo fittings, instead use the large thin hex shapes by sliding the rubber vibration dampeners away from them - again a largish Crescent wrench is required. The banjos are not particularly tight, what looks like crush washers are actually bonded o-ring washers. Remove the aft one first and expect perhaps 4 oz of diesel to come out - enough you will want a small cup. Encourage it to drain by tilting the aft end down and shaking it. Then remove the front banjo and you now have the pump free. With practice you are now about 1 1/2 hours in.
12) The new part number for the pump is 5260632 superseding others. I recommend buying directly from Cummins USA parts even at the high price, there seem to be many fakes about and there is too much labor involved to chance it as I did. While you are ordering this, get four new bonded sealing washers, 3963990. The Cummins price for all of that was $386. “Genuine Cummins OEM” pumps can be had on eBay for <$100, but ‘you takes your chance’.
13) Reassembly is the reverse. I reinstalled the pump and ECM plate, hooked up the wiring and fuel hoses, powered up the engine, and ran a few key on cycles - don’t start the engine - before reinstalling the aftercooler and fuel cooler. It should bleat that plaintiff tone for 60 seconds, then stop, with no errors indicated on Smartcraft. You can almost still check for fuel leaks at this time, they are pretty much buried later. Double check that all the bolts and particularly all the hose clamps are tight before you start the engine, and check again after a short period of operation.
