I guess the one thing that is normally ignored with a lot of these swaps is that very HD forks and swingarms, with wide wheel capability are being installed on frames that were not initially designed to take the twisting and braking forces now being applied.
I'd suggest that anyone who has done this might want to have some subtle yet valuable gusseting done on the frame. Up by the steering head is fairly common, with some aluminum plate being welded to both the upper rail and the cast lower piece, leaving a much smaller hole to allow the wiring etc to pass through.
Around the swingarm pivot, a decent sized plate can be done around the bolt whole, limiting the twisting distortion transmitted from a tougher swingarm and much stickier tires.
Given that a number of engine mounts attach via the lower frame rails, some welding up of strips to alleviate bending should help. Stop and think what the motor is trying to do with respect to the other pieces and you can pretty much spot where additions will help and where they will just add weight.
If you get a chance to leaf through the UK mag 'Streetfighters', you'll quite often see examples of what I'm talking about.
The stock lower triple clamp of the 93 water pumper is inadequate for the braking forces available from its front end. Pretty much the same thing as 91/92. The magazines shit all over the frames for the brake judder where in actual fact it is the triple clamp at fault. For USD forks, a trip to a non-criminal machinist should allow you to wind up with a 3 bolt lower without breaking the bank. This will stick the braking judder up the journos asses.
Basically, whatever you choose to mod and mix, you need to prepare to get surprised. The bike is a complete system, and while stock is NEVER the correct formula
, you need to go around the circle of the system to predict where the next 'bump' will come from. Half the fun is in learning how this shit interacts.....or screaming hell
!!!