Haven't found a fix yet, but I've got it to a playable state. You can adjust the screen position from WITHIN the game menu. Just start a game then pause it by pressing "Start" then "Select". You should see "Screen Adjust" and just move it. (the opponent side will be partially cut off, but that's not important
As for the speed of the game....There's two way to slow it down. One is by the Option WITHIN the game and the other is to set "AutoSpeed=on" in FPSE.ini to limit 50fps max.
Also, the D-pad sensitivity seem to be a problem with fpsece 0.10.1 release. For example, if you press a button and hold for 1 second the emulator will process it as 2 second (exaggerated example).