I installed a koenig on my S3 out of the box when that landrover was about 2 years old....(1975).... everything fit.
I can't imagine much change where that shaft goes, It does travel above the cross member.
If i were you i'd cram that shaft in there .......... I am assuming it runs off the xfer case? if not you're dealing with the shaft that runs the capstan winch. you'll get it to work after all this, let us know how it goes?