I've been using PhpED on my notebook for a year or so and I have Visual Studio-like IDE shortcuts there (eg. F5 to run the project). Now I need to migrate to other computer, but when I installed PhpED there, I have found that all shortcuts are from Borland IDEs (F9 to run the project etc.). How can I set all IDE shortcuts to VS-like short of changing them one by one? Alternatively, how can I copy shortcut layout from the notebook to new system? Could it be an option to choose keyboard mapping in older version of IDE? Cause I don't remember changing shortcuts one by one on notebook.

Editor key mapping presets may be chosen on Editor > Editor shortcuts page in Settings dialog (this will not affect IDE shortcuts such as "Run project").
Shortcuts along with some other settings are stored in phped.cfg file in (user)\Application Data\NuSphere\PhpED\config directory.
Also you may be interested in this topic: http://forum.nusphere.com/phped-settings-mgr-import-export-your-settings-t8608.html

Thank you. I am wondering how it happened that two installations have different IDE shortcuts out of the box. Am I mistaken or there was a way to choose presets for IDE shortcuts before?

Seems you modified shortcuts yourself and perhaps forgot about it.
If you want to copy settings, you can do this by copying files in %APPDATA%\nusphere\phped\config
All IDE-wide shortcuts are in phped.cfg file, in /root/IDEShortCuts xml node.