I'm late to the party, sorry about that.
I can tell you some about the 126 but it is by no means definitive.
My 126 is in a 93 FXR and it bolts right in. Header fit is tight but not a problem. Changing rocker box gaskets probably is and it looks as if the engine needs to come out.
All S&S 126 engines are twin cam but available in cases with Evo engine mounts, too. A wiring adapter harness is needed and an Evo ignition module will not work.
I already had a Baker 5 speed, so I can't say if the stock trans is OK. The 126 only took a couple pulls at half throttle and 4th gear to fry the clutch, a Barnett clutch that was adequate for a nasty 120 with ported STD heads and a 266* .650 lift cam. Took a week after that to fry the starter drive, and another couple months to get the next one and I use the fancy drives made in USA with a sprag. The motor will find the weak spots if you don't already know what they are and for that matter, it will find them even if you do know. I am using the S&S high strength drive belt and if (when) it goes I'll switch to chain.
I use RB Racing Pro Stock Spyder head pipes (I cut the muffler off) grafted to a 2.5" Supertrapp muffler with no disks. The Spyder muffler sounded like crap and cost both power and torque. Now power is everywhere. You don't get that big torque hit down low but it hits hard enough to spin the tire at any throttle more than about 1/3 in 1st gear, which is good. On rare occasions when the tire does hook up, the front tire comes up. So you end up replacing rear tires when the front has very little wear. At first I was hoping for more low end torque but then realist woke up and let me know that you really don't need any more torque than this in the FXR or Dyna, and if it had more you would get in trouble a lot sooner and deeper.
Power over 4K RPM and half throttle is scary. That 120 was pretty strong and this thing makes it feel like something was wrong with it.
The 126 needs a bigger pipe. I'm thinking a good step pipe. Star Racing suggests 2"->2.125->2.250, if I remember correctly. They want $1900 for their pipe, so I will make my own when I can. Or help a friend who has a TIG welder.
It needs a lot of carb, too. I used first an S&S G, then had John Sachs bore it from 44mm to 47. That was a lot better. Now I am running a Mikuni 48 and it feels better than either S&S but still held back. Star Racing suggested an S&S D carb but they are no fun on the street. Maybe when my rich aunt dies I can afford one of the hot rod shops to work one over and civilize it.
So, for you FI guys I don't know which throttle body is best, but I would guess 55-60 MM.
I had Star cut the heads for higher compression and port them. Can't say how much this helped, but I am pretty content with it now.
I didn't want to make this message about me, but I thought it might be important to post what I did and any ideas or reactions about what happened and if it might be better.
The lesson so far is that if this thing is to be optimum, then many areas need TLC. If you aren't prepared to go the whole route, then save some money and get a milder 120, 124 or one of the Ultimas. They have the big torque and aren't as fussy about pipes and induction.
There are many here with more experience than me, so listen to then about the nuts and bolts technical aspects. This is just from the POV of a recently destitute owner, an owner driven to the poorhouse by this thing letting me know which parts are inadequate.