Since I have already stated my opinion on this subject (as a Land Cruiser builder of quite a few years now) and you're still choosing to go ahead with an SR, then you should take the time to do it right.
If you are contemplating an SOA at some point, you should factor that into your build. There will be significant geometry changes if you're going SOA vs SUA with an SR.
The Land Cruiser Advanced Handling type kits (see the previous photos in this thread) offer you very little in the way of an advantage when driving in the rocks vs. just running shackles up front (normal configuration) since they stick down too far. So, if must spend your money on this rather useless and expensive conversion (my opinion) then you should try to do your best to recess all the mounting points as much as possible. Recessing the mounts, really does work better with an SOA since you will lose some of your lift by doing so. To offset some of the loss of lift in an SUA configuration, you should perhaps consider what your lift options are.
In reality, most of the very small gains in ride quality from going to an SR are simply from repairing what was wrong with the front axle and/or suspension in the first place. I would strongly recommend that you fix all of the things that need to be done with your front end now, before you complete the SR so that there is little confusion about what has actually been improved by performing an SR.
A few thoughts about suspension geometry:
You should aim to increase your overall caster angle as much as possible up the 5 or 6 degrees range. Adding caster to bring things in line with these numbers will improve road manners immensely. If you keep your front spring mounts as short as possible (and close to the frame) you will see some improvement in caster angle.
Seriously consider the possibility of adding longer springs to the front; a set of rear springs (with a little leaf shuffling to adjust ride height) could achieve this. Longer springs will provide for softer, more comfortable ride and you will gain a fair bit of articulated travel as well. You may need to change your shocks and/or mounts to handle the extra articulated travel.
The real (tried and tested gains) of an SR are a very slight improvement in how the truck will respond to small bumps and irregularities in terrain (eg: somewhat rough paved roads, gravel roads). The difference is somewhat like how the ride feels between running 40PSi on the street vs. 32PSI. In my case, it was the difference between the doors rattling a little or a lot; from the driver's seat, I can't say that I noticed much change.
In the years that my own truck was SR, I did not notice any appreciable advantages for fourwheeling (the whole debate about pulling for pushing your wheels over the terrain) and I feel that this aspect of the argument is pretty much rubbish. While I had the SR in place my truck was SUA, and I did not notice any benefits at all with respect to hitting rocks (it's a rare occurence for me anyhow) with the springs. I'm sure that if you spend all your time surfing the big granite slabs of the Sierras, then this could be a worthwhile conversion, but only if everything is tucked up as much as possible.
The one disadvantage that I found was that the (expensive) driveshaft that I had made up to handle the extra slip yoke travel wore out quite quickly (I was doing a considerable amount of fourwheeling at the time). When I went SOA, I removed the SR and went back to a stock driveshaft.
hope this info helps... but, ymmv.
~John