Sync vertical scroll between two windows

Solution 1:

I suggest you use AutohotKey for this. You then can try to

1. Listen for MouseWheel Event in either Application (Reader, Safari)
2. Switch focus to the other application, Send Mousewheel Event
3. Switch back

I Hope this is fast enough to appear "seemless"

[EDIT]

Here is the script I have made following this answer :

WheelDown::
SetTitleMatchMode, 2
IfWinActive, SafariTitle ; Replace 'SafariTitle' by the title of the safari windows
{
        CoordMode, Mouse, Screen
        WinGet, active_id, ID, A
        IfWinExist, Adobe
        {
                Send {WheelDown}
                WinActivate ; Automatically uses the window found above.
                Send {WheelDown}
                Send {WheelDown}
                WinActivate, ahk_id %active_id%
        }
}
Else
{
        Send {WheelDown}
}
return

WheelUp::
SetTitleMatchMode, 2
IfWinActive, SafariTitle ; Replace 'SafariTitle' by the title of the safari windows
{
        CoordMode, Mouse, Screen
        WinGet, active_id, ID, A
        IfWinExist, Adobe
        {
                Send {WheelUp}
                WinActivate ; Automatically uses the window found above.
                Send {WheelUp}
                Send {WheelUp}
                WinActivate, ahk_id %active_id%
        }
        }
        Else
        {
                Send {WheelUp}
        }
return

Solution 2:

Notepad++ has the ability to do sync'd vertical scrolling for plain text docs and source code - as do many other 'dev'-type document apps - but as slhck says it would help to know what you are currently using and what type of docs you are trying to view.

Edit: based on your useful feedback - here's a possible solution:

It's pretty straightforward to convert any doc to a PDF so if you get both docs in that format you can use something like DiffPDF to scroll through them both:

http://www.qtrac.eu/diffpdf.html (program description and downloads)

http://soft.rubypdf.com/software/diffpdf (Windows version)

DiffPDF can compare two PDF files. It offers two comparison modes: Text and Appearance.

By default the comparison is of the text on each pair of pages, but comparing the appearance of pages is also supported.