I looked at the hotkeys you posted. Some of them that I bolded are already in the guide.
I'll add Ctrl + H, Ctrl + PrtScr and Alt + PrtScr as these seem very useful. Other functions that can be done in one or more other ways aren't that important to include. As you said this page itself is already very cluttered. I also fixed the "resorces" typo.
• Scrolling through units with the MW (mouse wheel) requires Ctrl to be held; I don't think city cycling is possible with the MW.
• The flying camera toggle requires Alt to be held in addition to Ctrl (alternative: Ctrl+Backslash). Shift+Alt+F freezes the camera angle while flying.
• Alt+F1: Free Colonies
• Shift+D: Contact player (menu popup)
• Ctrl+PrtScreen: Hi-res screenshot (TGA format, uses two times the screen resolution it seems)
• Shift+PrtScreen: Enter file name for screenshot
• Alt+U: Toggle unit display ("Toggle flag units" to use the same lingo as for Ctrl+R. Oh, and typo: "resorces".)
• I: Intercept aircraft
• H: Heal
• Ctrl+H: Select injured units
• Shift+Ctrl+H: Hall of Fame screen
• MMB (middle mouse button) centers the camera on the currently selected unit or city. C will also center on either a selected city or unit (says only "center on unit").
• Alt+C: Select all units in tile
• NUM5 is an alias for C (with and without modifier keys), but, unlike C, cycles to the next unit when the camera is already centered.
• Shift+P: Blockade/ Plunder
• On vassal's name (scoreboard): Alt+LMB – Demand vassal tribute
• Shift+LMB on tile: Context menu (unless right-click menu enabled)
• Shift+LMB on unit order: Add to the end of the queue
• Num0: Skip unit's turn (unlike Space, this can't end the player's turn)
• Numpad+/- is an alternative for city cycling, Numpad star and slash for unit cycling. Numpad period for Fortify.
I'll add Ctrl + H, Ctrl + PrtScr and Alt + PrtScr as these seem very useful. Other functions that can be done in one or more other ways aren't that important to include. As you said this page itself is already very cluttered. I also fixed the "resorces" typo.