IMO, the differences in recoil between a 9mm and .40 are negligible in the XD series. Some of my friends' wives shot both one day at the range and while they noted more differences than the guys did, none of them had more difficulty controlling the .40 than the 9mm.
I have not yet held or shot an XD(M) although I have shot most of the other offerings excepting the .357 sig chamberings. From the videos and literature on the XD(M), if I were in the market for a .40, it would be on my very short list of pistols to check out. I appears thus far that SA has fixed the few troubling areas of the XD, most notably the trigger (although there are fairly inexpensive aftermarket solutions to the things people don't like about the original XD triggers).
I carry an XD45 usually and like it very much so I am biased in that regard. The only FTF or FTE I have ever had with any XD was ammo related. It is, IMO, an excellent, durable pistol which appears to have properly evolved with the XD(M) model.
Having never shot the cz, although I have held one, I cannot give a direct comparison.