The early steel S tube installation uses the straight in ported wheel cylinder. The steel S fastens to that port and the flex hose at the top support bracket on the knuckle. The outboard end of that hose is secured in that bracket with the "C" clip. This clip is a common brake hardware item I have been purchasing across the Carquest and NAPA counters.
The late brake installations 10" use a different Steel S tube. They do use a wheel cylinder with an angled port and a different hose support bracket since the hose goes upwards to the frame instead of downwards to the axle housing. This is because the 10 and 11" brake jeeps run the tube that connects the left front brake to the right front brake across the crossmember under the radiator instead of down on the axle housing.
The 11" brakes systems introduced in 1972 run a flex hose directly from the wheel cylinder to the frame bracket where the "C" clip is used to retain the hose and tube at that point on the frame.
So if you leave the transverse (left to right) brake tube on the axle housing you must insure that the flex hose remains protected in the original M38A1 tray/bracket. As long as the hose lies in the bracket/tray and is not exposed to damage from the axle travel bump stop you will be fine. As John mentioned above the important thing is to make sure the flex hose length you use is not too short or too long based on your jeep's axle flex/travel and steering travel and does not strike anything during those travels.
If you want to keep it as simple and correct as possible then you should adapt the entire 1972 front plumbing to your M38A1. This way you can use the off the shelf hoses for the 1972 to 78 CJ5 and fab a pair of "C" clip brackets for the frame rails above the axle in the same spot they go on the 72 CJ5.
See the stock vs 10" photos here:
http://www.willysmjeeps.com/v2/modules. ... hp&page=23
