i swapped in a manual trans in my 79 f250 4x4 about a year ago. i had the trans gone through before i put it in. I installed a new luk clutch, resurfaced the flywheel, new throw out bearing, etc.
Ever since i installed it there was always a clunking noise in the trans. i drove it and didnt think much about it untill recently where im just fed up with it. the trans always shifted nice and tight with no grinding.
In the past few weeks i picked up a parts truck for the trans thinking thats what my problem was. I drove the truck before i pulled it and it mad no noises whatsoever. I had it gone through and reasealed it before i installed it. I pulled my old trans and it still looked good with no slop on the input shaft(which i thought that was the problem). I installed the new one and once again same noise.
I decided to pull the trans again this time pulling the bellhousing and checking the clutch. It looked like new to me still and i saw nothing abnormal. Put it back together and still the same. I swapped the transfer case too, checked both driveshafts all is good. Im thinking its coming from the bellhousing(maybe the clutch is bad)
so here is a video and you can hear what im talking about it happens mostly when i engage the clutch and i am coasting. it is much louder now with no carpet and the trans hump cover off.

Np 435 transmission clunk - YouTube

 

Only a guess, loose flywheel, loose/wrong starter, frozen front driveshaft slip joint.
I can see why it is annoying you, hope you find the problem.

 

flywheel is good, i just installed a new starter to rule that out and the front driveshaft is new and the rear has been gone through with new u joints and re balanced. Ive tried driving it with the front shaft only and same with the rear and it doesnt make a difference. I just ordered a new clutch that is about the only thing i havent changed. any one else have suggestions?

 

Any vibration?

Pilot bushing wrong perhaps?

Clutch fork loose or TO bearing not quite on right?

OEM length bolts used to bolt trans to bell? Or longer ones that just might kiss something? (a real wag there)

 

Any vibration? no vibrations

Pilot bushing wrong perhaps? nope its right it came with the clutch kit

Clutch fork loose or TO bearing not quite on right? clutch fork has normal tension and its hard to tell if its on right but when i pulled it apart it looked fine

OEM length bolts used to bolt trans to bell? Or longer ones that just might kiss something? (a real wag there) used oem bolts

 

Is there an adapter shaft between the transmission and transfer case?


I have seen spline wear that could cause this.

 

T/C mounts to left (drivers) side frame rail using two rubber 'donut' insulators. Both could be soaked with oil to the consistancy of a wet sponge or have age cracked/disintigrated.

 

What is the operating conditions of the truck in the video? Second gear, on the street? or on blocks? ..etc?


maybe onto something here, definitely something interfering ..you have replaced a lot of parts and the problem is still alive ..look at the parts you have not replaced lately. Pull the boot from around the clutch fork and see if you can look inside the bell-housing ..the clutch bolts may be contacting the housing because of end play in the crankshaft.

 

In the video I'm driving the truck in second gear coasting and it's clunking when I'm pushing the clutch in.

I will check and see if I can see anything through the boot but I don't think the bolts are too long because I bolted up the bellhousing to the trans while It was out and the bolts didn't stick through

 

Yes it has a married tcase splines are good.