The position of the timer is not important, what is important is the position of the injection pump when you tighten the left hand thread bolt. When this bolt is tightened the IP pump should be locked at the assembly point and the engine should be at 15ATDC.

I don't think I'd try this job without the proper factory tool that locks the pump into place - when I bought mine it was only $25 from the dealer.

I don't see any reference to the the left hand thread bolt being a stretch bolt or loctite requirement upon re-assembly, the assembly torque spec is only 40-50 NM. I reused my bolt and did not use loctite.