I assume this same process will work for Ctrl as it did with Alt for me. Just be careful when testing the keys you assign using xbindkeys-config.
I read this https://help.ubuntu.com/community/KeyboardShortcuts which helped me figure out the following. While the xautomation package that includes the xte tool might be used instead of xvkbd to emit the key codes I used xvkbd to do the same thing.
sudo apt-get install xbindkeys xbindkeys-config xvkbd
xbindkeys --defaults > /home/your-user-name/.xbindkeysrc
For some reason this added a binding for ctrl-f that I had to comment out. While perhaps a useful default example I need ctrl-f to find inside of web pages.
After figuring out the "keysims" of Prior for PgUp and Next for PgDown this wasn't too tough. Running and using xbindkeys-config resulted in the following entries in .xbindkeysrc for me.
#alt-up
"xvkbd -xsendevent -text "\[Prior]""
m:0x18 + c:111
Alt+Mod2 + Up
#alt-down
"xvkbd -xsendevent -text "\[Next]""
m:0x18 + c:116
Alt+Mod2 + Down
when using Ubuntu 12.04 precise pangolin after creating the .xbindkeysrc file it was detected and the xbindkeys program was run automatically on my next login.
So this should do what you want.
#ctrl-up
"xvkbd -xsendevent -text "\[Prior]""
m:0x14 + c:111
Ctrl+Mod2 + Up
#ctrl-down
"xvkbd -xsendevent -text "\[Next]""
m:0x14 + c:116
Ctrl+Mod2 + Down