Originally Posted by
rccardr
It is possible that your problem is related more to 1) your Sora FD (which I am going to assume is being shifted by an STI and not a down tube or bar end friction shifter), and 2) the change in chainring size. I know that Shimano STI shifting systems tend to be very sensitive with regard to chainring tooth count, and even though 39 to 42 teeth doesn't sound like a lot, it may be just enough to confuse your FD.
I experienced this personally when trying to improve the shifting on my Voyageur: it balked badly between the middle and inner gears as a 50/34/24 and after trying multiple FD's would only make the shift if I was four gears down from the largest cog, but it now shifts perfectly every time in every possible gear combination using a crankset with the 48/36/24 chainrings for which it was designed. So, there's that.
There's also difference in chainring ramps and gaps profiles. 42-52 combo doesn't use the same profile as 39-53 one. The old standards of Shimano chainring labeling were A and B. Now they have also M (for MTB I guess), T for trecking, FD, NB and loads of others. Combining two (or three) different labels on one crankset is not advised - sometimes it works better, sometimes worse. Some explanation can be found here (A, B and E types at least):
The Truth About the Shimano A and B Type Chainrings - The Tall Cyclist