I was recently messaging another member on how to re-time a 6.9 and located this fairly useful document on how to do it...
The engine manuals describe the usual method of aligning the timing marks on the crank gear, cam gear and injection pump gear with the the front cover off. This is great for engine assembly, but is not too helpful if the owner has made the rookie mistake of removing the injection pump gear housing to remove the pump. Many novice owners have ended up selling their trucks because they could not figure out how to get it back in time without disassembling the front of the engine. Maybe this document will help out a member some day if they goof and pull the gear housing on their truck:
http://www.blackwire.com/~bjordan/Tech/Timing_the_6.9-7.3_IDI_101.pdf
SHORT BED 4-DOOR DIESEL: 1986 F350 4x4 under construction-- 7.3 IDIT ZF5+GVOD
STRAIGHT SIX 4X4: 1981 F150 2wd to 4x4-- 300 I6 close ratio diesel T19, hydroboost brakes, Saginaw steering
BIG F: 1995 F-Superduty under construction— converting to 6.9L IDI diesel ZF5+DNE2