Instant Sheller definitely fixes the first two issues. And now that I think about it, I think I had an issue where Mala would lose focus, also. For me, after I ran Instant Sheller it fixed itself. My guess is that there was some other windows task bar related thingy that was running, and after I ran Instant Sheller it was not an issue.
If you can plug in a keyboard and mouse without too much trouble, running Instant Sheller isn't really something to be afraid of. You will run in, pick your boot screen, tick the boxes for the options you want fixed like mouse cursor etc., then click Go an reboot. If you ever want to undo it, you would plug in your mouse and keyboard, hit ctrl-alt-delete and run the task manager. From there you can run apps form the File menu. If you run explorer.exe, then you can use the mouse to navigate to Instant Sheller, run it again, click Undo, and then reboot. The only issue is that before you undo Instant Sheller, your mouse cursor will be a tiny black dot, so it is very difficult to see - but you can.
I say go for it, and see if the focus issue resolves itself. As for the Focus Logger plug in, I believe it was designed to merely tell you what application was stealing the focus. I couldn't get it to tell me anything either.
And finally if you need it, instead of having AHK simulate a mouse click, I have read that you can simply have it check if an app (Mala) is running in the foreground. If it isn't, AHK can set it to the foreground. But you would have to search on that, cause I don't know for sure.