Thank you all for providing helpful tips on getting the job done. I am, with all your help, at the point where I can fill the PS fluid, get it bled and test my work out.
This much is sure, if I have to this job again (aaaaagh God forbid) I will definitely pull the spindle out in the beginning, much easier to pull or reinstall the steering box, plus no chance of messing up the steering spindle.
Other than the steering box, one more thing that I have noticed odd with my car is that the steering spindle extension requirement does not match the shop manual. In the shop manual the upper inspection hole closer to the steering wheel is for cars with power steering, where as the lower one for mechanical ones. But on my setup if I use the PS length the spindle is not long enough to reach the coupler, so I have to use the mechanical setting (In the manual they are represented by 15a and 15b respectively). Has anyone come across this situation before? I am thinking this could potentially be because of the odd ball steering box fitted on my 6.3.