Then run starter for 30 seconds.   Engine won't start, and shouldn't.   Turn off key and let starter cool off for two to three minutes.   Then run starter for twenty seconds.   Engine will start.   It will run rough, so give it about
quarter or half accelerator until it smooths out.  Then things will be fine.
It is VERY IMPT that you follow this procedure EXACTLY and USE A STOPWATCH, as timing is CRITICAL!
For the B5.9 engine, the procedure is different because this engine does not have an electronic fuel pump.   The following is from Lew Parsons of Cummins:
If you do have the older 230hp B-series, there is only one way to
clear air from the fuel pump and injector lines.  You have to loosen the
fitting (where they enter the head) on the injector lines and crank the
engine with the starter and literally pump the air out of the injector
lines.  This is not an easy, or very clean thing to do.   And it is a (2)
As you can imagine the fuel is under pressure and can spray for quite
some distance, (all over the bedroom) so you have to keep a rag over the
fitting while the other person is cranking the engine.  The idea is to
"crack" or just loosen the injector fitting and allow the fuel pump to push
the air bubble out, then tighten the fitting again and move on to the next
injector line.  The B-series is a (6) cylinder engine, and will have (6)
injector lines, one for each cylinder.
In my experience, I have rarely had to bleed all (6) lines to get the
engine to start.  Most of the time, I'll bleed the air out of cylinder #1, #6
then #3 or #4, and the engine will start to "sputter" like it is trying fire
while I'm bleeding the air out.  When that happens, tighten the fitting up
and let the engine start.   This last part is very important!
Once the engine has started, push the accelerator pedal to the floor and
hold it there for 30-60 seconds.  Doing this allows the fuel pump to pull any
remaining air pockets out of the filter and fuel lines without stalling the
engine.  If you let the engine idle, it will not have enough suction on the
fuel lines to pull past a air bubble and will stall it out again.
That is probably why your engine stalled out in the first place after
you drained the water out of your fuel filter.
Gene Hamelman also advises that it may be possible to just crank the engine for 30 seconds, let the starter cool, and crank again and again until the engine starts.   Just be sure to let your starter cool sufficiently between successive starting attempts ( 2 minutes if I recall right??).
Jim Kangas called the 1-800-DIESELS number and got this info from Cummins:
There is a manual pump on the right side of the engine
(230 HP) under the engine mounted fuel filter.   Fill both fuel filters
with fuel and then pump the button on the manual pump until it got hard (like
an outboard motor fuel line bulb).   It took 200 pumps using both hands to do
it but the engine started right up.   You don't have to do the
pumping consecutively, you can take a break and not lose any ground.  This is
easiest to do laying on your back under the engine.   It is not that difficult
Here is an alternative method provided by Bud Himes:
First, raise the bed and engine cover and locate the banjo fitting an the
engine-mounted fuel filter.  Crack it loose about 3/4 turn.
Make sure the new filter (or the old one if you lost the prime while draining
water from the clear bowl on the bottom) is full of fuel.
Next, remove the fuel cap and replace it with the tank pressurizer seen in
the following photos.   Click either picture for a larger view.
I made it out of parts I had in my shop, but you can
buy the parts you need for less than $6.00, Ignore the pressure guage on
mine - I also use ot on my farm tractor and its there to remind me not to
pressurize more than 15psi.
Actually all you need it the forward end, from the guage forward.
The cap is a STANT 11817, which you can get from any auto parts store.  Drill
a 3/8" diameter hole straight through the middle.
Next, pick up a six inch 1/4" NPT galvanized nipple from the hardware store
and thread it through the hole, making sure it goea all the way through.
On the end that comes out the bottom, use a 3/8-24 nut.  It's not an exact
fit, but close enough.  Put a little hot glue or some sort of sealant under
the nut and pull it back through the cap until it seals.
The thrads on the other end will fit most air guns.
Once you have the pressurizer on the filler neck, and an air compressor and
gun hooked to the pressurizer, gently put air in the tank until it "Pops" -
more like a booming sound, actually.
After several seconds, you will hear the same sound when the pressure bleeds
off, so have whoever is helping you give it another gentle shot of air.  And
keep doing it until the engine starts.
Meanwhile, back at the banjo fitting, once you start getting a steady spray
of fuel from the fitting, close it.  Not too tight.  About 20 punds of torque
is about right.  Also have plenty of rags handy to mop up the fuel.
Next, turn on the ignition key, wait five seconds and "Bump" the starter.
Leave the key in the RUN position for 30 seconds, then turn it off.  Do this
at least five times or more, but ten should be plenty.
Then turn the key on and activate the starter until the engine starts.  Go to
about half throttle and keep it there until the engine runs smooth - about 5
to 10 seconds, then let it go to idle.  You should not have a lot of smoke
excepy during the first five seconds or so.And remember that the next time
you drain water from the filter, have the engine running while you do it, and
don't open the drain valve too far.
If you have questions, contact me at firstname.lastname@example.org