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Not really sure what you are asking. The bellhousing has nothing to do with the engine. However if you are asking if the manual transmissions offered with the 6.9 engine had integral bellhousings then the answer is no, the bellhousing was seperate.
If you are asking if a ZF5 from a 7.3 will bolt up to a 6.9 then the answer is yes.
Thanks guys I did say that in a confusing way, it made sence because I was the one makling the question. But you did answer my question I was wondering if the 6.9 manual trans was a one piece bellhousing/trans, like the 7.3 trans. So the 6.9 transmission has a seperate bellhousing from trans. Correct?
You are going to have to "basically" get a pressure plate for a 6.9 application and get a clutch disk for a 7.3 application to fit the input shaft on the trans. You are going to also have to take the throwout bearing fork and weld up the points of contact where the fork hits the throwout bearing. Going to have to weld it up about 5/16 to 3/8 of an inch because the flywheel housing is deeper on the ZF. I have done this a few times. There may be an aftermarket clutch kit to do this now but back when I did these I had to go to a clutch shop and have the disk made for it...It isn't to much trouble.
When I did this swap on my 85 4X4 I had a 93 donor. I used a single mass flywheel conversion from NAPA for a 93 7.3. It contains the flywheel, clutch disc, pressure plate, throw out bearing, pilot bearing and all new mounting hardware. Everything is a direct bolt up. I used the throw out bearing fork from the 93. The 208 transfer case from the 85 bolts to the ZF5 and the dirve shafts did not need altering. I used the floor hump panel from the 93 as the ZF is a little taller. I had to cut a new hole for the transfer case shift lever as it mounts different on the ZF. The lever came from the 93. Everything but cutting the new hole for the tc shifter was a direct bolt up.