I have 10 speed Shimano on my touring bike. Triple crank. I'd suggest going 10 speed cassette. 9 is slightly old, outdated, and the 10 works perfect. So no rational reason not to have one more gear. You are buying everything new, so get the newest, most up to date components. As DaveB said, there are some compatibility issues between road STI shifters and MTB derailleurs and speeds. I have some 105 STI 10 speed levers and a very cheap 9 speed Deore rear derailleur. Might have cost all of $20 for the rear derailleur. So its real easy and cheap to make things work right.
As for gearing choices, I like about a 4 to 1 high gear. So 44 chainring and 11 cassette. 42x11 is also close enough. Your 40 outer ring choice would not be my choice. For the inner chainring, smallest possible no matter what. For your cranks it is 22 tooth inner chainring. 64mm bolt circle diameter. Its very easy and inexpensive to replace the inner ring on a crankset if the outer and middle are your preferred choice. And biggest cassette cog possible, sort of, on the cassette. Cassettes for 9 and 10 speed have either 32, 34, or 36 for the biggest cog. 32 and 34 will work with about all touring bikes no problem. The 36 may be too big on some touring bikes. Have to try it to find out. The rear derailleur upper pulley will not be able to get under the 36 cog. Likely due to the rear derailleur hanger not being long and low enough to allow the pulley to get under the cog. Works for 32 and 34 big cogs, but not enough clearance for the bigger 36 cog. But whether you have a 32, 34, or 36 big cog, does not matter because it amounts to about 1 gear inch difference between each. Tiny.