Hi Lambert. Not much to add once you've seen/read/understand my friend Mike Martin's "how to" article (also covered here, including video:
http://www.st-riders.net/index.php?topic=942). If you're registered at ST-Riders.net you can also see the tools that have been put together to do the upgrade or just remove and replace (R&R) the old oil-cooled alternator system that was used on the earlier models of ST1100s:
http://www.st-riders.net/index.php?topic=545.0
You mention 4 bolts for your "alternator shaft" assembly, which leads me to believe you have one of the early models' oil-cooled versions as the later models' automotive type, air-cooled alternators (aka, "40amper") only use 3 bolts to secure its version of alternator shaft assembly to the engine case. If that's the case, there is nothing to really fail in the early models' alternator shaft assembly and no need to even pull it out of the engine, disengaging its two split gears' splines from the flywheel splines. The other half of the system, the Stator is all that needs to be removed. So I'm curious as to why your alt shaft assy was removed in the first place...?
That said, in any case, now you're experiencing the common problem of getting the alternator shaft assembly (either old or newer version) inserted into the engine case while aligning/sliding both split gears' splines onto the flywheel's splines. The shortcut way developed by Jon Lewis years ago was to pull the ~6mm "pin" that aligned the split gears out with a wire through the oil drain plug hole, versus the Honda Service Manual's method of dropping the mufflers and oil drain pan to extract the alignment pin with a pliers after the alt shaft assy was fully seated.
As mentioned, if using the Lewis-Pin method be sure to keep the pin aligned with the hole in the engine case to ensure the straightest pull forward and out the oil drain hole. I recommend everyone do a "bench test" of pulling the Lewis-Pin out, prior to the actual insertion. Jiggling/rotating the whole alt shaft assy may help getting the split gears on if they're not sliding "home" easily. Take your time and don't force it. Do not tighten the bolts in an attempt to force the alt shaft assy fully seated. Something expensive will break, as a number of alt upgraders have learned the hard way. Stop and take a break... try again later.
If the Lewis-Pin method simply isn't working for you, at some point just make the decision to quit that and resort to the shop manual method.
Good luck. [I did get your email...]
Regards, John