Converting to 40mm carbs is a bolt-up operation, but a lot of parts are involved. Do yourself a favor and simply buy them all before you start to work on the bike.
The parts you need will depend on the throttle system your bike has. The four throttle systems (details here) are basically:
Additionally, the choke cables for handlebar-mounted chokes are different. Airbox-mounted chokes don't need modification.
For bikes with the K-type switchgear, the 40mm carbs require unique throttle cables with extra-long inner cable. This is because the K switchgear requires longer cables due to the way the cables enter the throttle housing, and the 40mm carbs require longer cables because the span from the carb top to the lever is longer. Add the two factors together, and you get double-longer cables only applicable to '91-on R100R/GS with 40mm Bings. However, they won't be widely available in the US. If you modify the way the cables enter the throttle housing, and put the locknut under the carb top if needed, you can probably use standard (long) cables.
40mm carbs also take unique choke cables, from the splitter box down, due to the same size issue at the carb. This can also be worked around with modifications, but it's easier to just buy the correct cables.
For bikes with K-type switchgear (GS/R/M 91 and later) there are only two cables with enough exposed inner cable:
Bikes without K-type switches and with twin throttle cables (85 and later) can choose from several. The original application is listed, although the cables are functionally identical:
Bikes with single throttle cable and splitter:
Lower choke cables for handlebar-mounted choke:
The 40mm carbs have longer throttle arms (25mm rather than 20), requiring more cable travel to open. The standard throttle cam will not always fully open the 40mm carbs. The 40mm throttle cam has an extra ramp at the end to take up the extra cable.
Possible workaround: you could probably install the throttle arms from the 32mm carbs and do away with the 40mm cam, but the throttle actuation will be different; more throttle takeup at low openings and less takeup near full throttle.
The 40mm carbs require 40mm intake spigots on the heads. For conversion, the easiest way to go is to buy the 40-to-32 intake spigots. With the head hot, unscrew the old ones with a pipe wrench and thread the new ones in. Use a flat metal plate to tighten the new ones in (they have slots for this purpose).
You'll also need the 40mm intake rubbers and elbows. The upper elbow dimension is the same as the old one, so the junction with the airbox doesn't change
11 12 1 338 361 32-to-40mm intake stubs
13 72 1 338 362 40mm intake rubbers
13 72 1 262 787 40mm intake elbows .
The 44-64 clamps used at the airbox sleeve are barely large enough to fit around the 40mm intake rubber. I found the 64mm clamps from the Oilhead to fit nicely. In fact I liked them so much I used Oilhead clamps elsewhere.
For square-airbox bikes, the intake snorkels should be changed so that both are large. 32mm bikes have one large and one small; the large snorkel is not available separately but the entire cover 13 72 1 337 228 (with two large snorkels) is only $20 at this moment. Note that in production the use of this cover is inconsistent, and it was not used on the later European bikes with 40mm carbs. However, I do think it's a worthwhile upgrade for any 40mm R100.40mm conversion