If by switch box you mean the stock Triumph switch housing, you have to cut it up to get the hydraulic MC & level to fit.
Point 76 in the R3Owners guide;
72. Run the supercharger outlet hose across the front of the engine, tucked under the lower radiator mounts, and up over the engine coolant expansion bottle, under the left chassis spine to where the oil filter will be 73. Fit the oil filter, taking care to have it in the right direction...
While you're at it, can you post a pic of the clutch MC & lever?
Wondering if they're still supplying the el cheapo chinese junk from Amazon, or have upgraded.
Would highly recommend getting a Triumph hydraulic clutch MC & level from say a Sprint or something. You just have to ream out the bar clamp to 1" but after that it's perfect looking & reliable.