Personally I would get a later set of Showa forks specifically for the SS to save all the above hassle! Alternatively get a set of later Monster forks (you could even go radial) and just put them through the yokes more to get the same ride-height. On my old 600SS we went to the later Showa forks (65mm calipers from the original 40mm spaced Marzocchis) as they were a straight swap, but depending on the year you need to change the front wheel as the axle is a different size. You can easily fit a 916 front wheel though! Also, as I've just put 1098 forks onto my 748, although the mounting holes for the mudguard are the same pitch, the mounts are not the same width apart so my 748 carbon one pulled in too much on the 1098 forks and started to crack. I managed to pick up a 1098 carbon one off ebay very cheap and this fits much better without the bowing. Having changed forks on both an SS and a SBK, my advice would be to use as many stock components as possible to save messing around with machining stuff, as it's a nightmare to get right and replace.
I tried to get 900SS forks the later ones, but they come up for sale once in a blue moon and people want quite frankly a stupid amount of money for them. The stock Showa shocks on the SSie are pretty rubbish though. Don't forget you may need to space your calipers out, I had to make 5mm spacers for fitting the 999 forks. Machining is near enough inevitable though
Yes, the 900ss (at least the carb version) stem is pressed in to the bottom yoke. I'm sure there are those that could un-press it, but that was too much to entertain. The 999 one is held in with some thread locking compound, so though unthreading is a neck-bulge challenge, once it starts, its easy
