Machining a little off both faces of the manifold & retaining the original angles should be ok if you realy need more clearance,dont take too much off the head side as the center is already quite thin & don't be tempted to alter the angle, especially to lower the filter end as this will result in the suction chamber contactng the frame webb. As I said earlier, you realy don't need much clearance & looking at your pics, you have plenty !!
The throttle linkage will be fine with a tweak of the opperating lever, when I can work out how to do it I'll post some pics of mine, as I said, I have done almost 30,000 miles on this set up & have had NO problems !
Topping up the dashpot without removing the tank is something I have learned along the way, there is enough room to unscrew the damper rod & push it to one side, then, with a small syringe & length of tube I basicaly fill to overflow then draw back on the syringe to suck out the excess, Easy !
As you have the kit why not give it a try ? I wonder how many of the naysayers have had experience with this conversion ? To answer your original question, In my experience, it's well worth "bothering with", I'd not use anything else.