Has anyone got a distributor for a 5.9 Magnum laying around they could measure for me? I need the measurement from end of shaft to mounting flange bottom.

I am building the engine for my 2001 Durango RT which I bought in December. It was running, driving but had leaking rear softplugs. Decided to pull it down and rebuild it. I never drove it myself other than when it was unloaded in driveway. Was very sludged up. Had been a poor factory reman engine installed in 2002.

I have it back in truck, still need to put intake,distributor,etc back on it. Now for the problem!
The distributor is the one that was in the Durango when I pulled it down. It will not sit down all the way like it should. It just barely starts into the bore, then is bottomed out in the drive gear as it should be.I do not recall if it was correct when I pulled it out to do the rebuild, but I did pull it out with no prying.

The distributor sits about 1/4 to 3/8" too high, oring sits about 1/8" above bore. I pulled the drive gear back out today to make sure it was seated all the way. It is sitting down on the bushing as it should.

I measured from top of gear to top of block, it measures the same as on old 318 I had laying around. Either 3 3/8" or 3 5/8" ( I'm at work and can't remember for sure).

Is it possible I have a wrong distributor from another engine that runs a longer shaft? All the info I can find so far seems to say that all LA/Magnums are interchangeable?

la and mag are the same.
so if the 318 was the same, you have the correct distributor.
why it doesn't fit?

It appears the shaft is too long, but I don't have another one to check. The bore size is correct, it sits down into bore slightly, but not far enough. Drive tang is fully seated in drive gear.

I have seen on the sludged motors that the oil pump shaft won't want to come out, you have to really pry it out hard. it is from carbon and deposit build up on the shaft and oil pump drive bushing. I assume you took the block to a maghine shop and had the block hot tanked and clean? also if using the oil pump shaft from the sludge motor, pull it out and clean it really good on a wire wheel bench grinder. If the motor wasn't hot tanked, get an engine brush and clean the oil pump shaft bushing. Also clean the oil pump shaft where the dizzy shaft goes into it and clean the dizzy drive tip.

When you rebuilt it, did you have a new intermediate bushing installed? If so, you might make sure it is properly installed and seated completely. If not it would keep the intermediate shaft from being at the proper depth.
Edit: Just saw where you measured from top of gear to top of block with same results as your spare 318. I would start over rechecking everything again. Please update when you find it!

I went to O Reilly's this morning and measured a new distributor, it measures the same as the one I have. This puts me back to the bushing not being right. It is the original bushing, but I did start to drive the intermediate shaft up from the bottom to remove, before I cleaned off the varnish on the lower shaft.
I am going to lift the shaft out tomorrow morning and take a real close look at the bushing. It almost has to be up from the block instead of being seated down. When I measured the old 318 I had I just did a quick measure, so may have erred on that.

I found the problem this morning. I took the intermediate shaft out, checked the bushing- it was all the way in as it should be. I applied a blob of assembly lube on top of the bushing, installed shaft- was going all the way down to seat on the bushing as it should.

I decided to take another look at the 318 I had. I started scraping a little gunk off top of gear to measure again when I realized what was going on.

The gear on the intermediate shaft has slipped down so it is flush with the top of the shaft. The shaft should be recessed down so it is 1/4" or so lower than top of gear. There is no roll pin to hold the gear in place, it appears to be press fit. That is why all my measurements were the same on my 5.9 and the 318! I was measuring from top of gear.

I pick up my new one from Autozone later today when it comes in.
Thanks for the feedback!