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I have a early fording system on my 38, the fuel pump has the primer handle, where the primmer handle attachs to the pump there is a vent like on the front and rear ends do I leave this vent or do I cap it off so it does't take in water when swimming buzz

The vent should have a built in check valve. The priming handle was not stock to the M38 fuel pump. It's an M38A1 thing. But you will see quite a few today on both jeeps. If you intend to actually "swim" deep ford your jeep you would be wise to upgrade her to the later sealed venting system.

I tried to up grade to the later I had it all hooked up w/ the later bell housing but the starters are different one early one late went to bolt the starter up and no go the holes were further apart come to find out the fly wheel is different between the years one has more teeth one less so all the money wasted buying parts going to try to sell them at aberdeen so that doesn't answer the question plug the fuel pump up or the axle vent buzz

I already answered that question. Read my first sentence again!

If you get dumb and plug the vent you will have other issues!

would it be better to run the vent line w/check ball to the transfercase and around to the air cleaner buzzz

That's what I would do if I planned on swimming the jeep.

thats what I was thinking last night thx for your time and support goimg to aberdeen buzz

This time of the year is my business (I am a self employed aircraft mechanic) which makes any recreational time very scarce. I usually can't get loose until July/August.