I am having a driveshaft issue on a cat with a driveline style Number Six. The engine is offset 6 degrees up and 6 degree over. Driveshaft is about 15" total. I have a digital protractor to set the vertical of the transmission and transom assembly flanges and they are both within .2 of a degree. So that is good. How to square up the engine with the transom assmebly so the flanges are straight horizontally?

It sounds like you are on the right track. Six degrees is about the maximum recommended true driveline angle, but I have seen higher. I would have to think about it a bit and do some math to know what the maximum driveline angle would be with 6 over and 6 up.
You are checking the flange to flange angles correct for easy direction. What I do for the other direction is to clamp as long of a straight edge as reasonable to both flanges and get the measurement on both ends of the straight edge as close as reasonably possible. I don't think it is real fussy, but of course the closer the better for driveline and component life.

Some digital protractors are also digital levels/squares. With that tool you should be able to lay the tool on the flange at any angle (vertical, horizontal or any combo) for comparison.

6* is a big number....You may want to check the drive line for balance.....new U joints...."tube harmonic cardboard"....sometimes misalignment is the only way to kill harmonic vibration......beyond that start at the crankshaft CL and check the flywheel, drive plate, bell housing ,transmission input/output for centered.

I am being told by the driveshaft builder 6 degrees is a lot. I am also being told by boat builders it is not. Some cats are running much steeper anlgles.
I did the bar stock clamped to the flanges last time and I thought it was dead on. I have managed to break two drvieshafts on the same side. Something is wrong.

I agree that something is wrong. I have seen boats with at least 6* and 1400 hp with no problem. Some misalignment is preferred. Just like in cars, the driveshafts are not perfectly straight. This stops flat spots from forming on the needle bearings by keeping them spinning.
Did you feel any vibration before they cut loose? Could they either have not been balanced correctly or threw the weights off?
Eddie

Brad, I had a customer use a digital protractor once that made a simple error that broke 3 driveshaft’s in a row.

He had zeroed the protractor on the transom assembly flange, then turned around and put it on the engine flange. He should have used the opposite side of the protractor, not turned it around.

After that to avoid confusion in my shop we would level the boat so the transom flange is actually at 0 vertically.

I do like the bar stock on the flange, I made a pair of hubs that would bolt to the flanges, held 1” aluminum rod. Easy to measure and see if they are parallel.

Are you saying 6 inches up and 6 inches over? Or 6 degrees measured at the flange?

What series driveline?

John Arruda may have a drive line isolator that would eliminate the slip joint/shaft and even U joints. Marc makes a good point, is it 6 + 6 inches or 6+ 6 degrees ? As I recall, it's inches.

As Marc asked, what series driveshaft/crosses are you running, 1410, 1480, or other? Unless it is a very old Six transom, the flange on the transom will accept either a 1410 or 1480, but it needs an adapter plate to use the 1410 because the pilot diameter is different. I have seen some mistakenly not use the adapter plate thinking the bolts will hold it centered, not so. I would run 1480's. There are different flanges available on the transmission depending on the source. If you have the 1480 series, where did the driveshaft break, at the slip joint, crosses, or tube? Is the driveshaft assembled with the joints in the correct alignment? Some driveshaft slip joints are not keyed to keep them correct and if taken apart can be mis-aligned. If the breakage is at the slip joint, there should be larger slip joints available.
I assumed that you meant 6 degrees. The angle vs position is very important, 6"x6" at a 15" flange to flange is a very high angle, 6 degrees of max angle (it doesn't matter which direction) is probably ok, but at the high side already.

Side bar on Brad's post and Falcon's reply. Can someone post a picture of the driveshaft with the u-joints in the "correct alignment". I may have a similar issue. Thanks

I'm of the opinion, several boats have a similar problem, some just more obvious than others.

Marc is an authority on the importance of "dialing in the bell housing" , an often overlooked procedure. While the procedure is only one component, it plays a serious role.