E   E1  A   C#m  B    F#m  G#m
E  ----0---0---0---0----0----0----0-
B  ----0---0---3---2----0----0----0-
G  ----1---9---3---1----4----0----0-
D  ----2---9---3---2----4----4----6-
A  ----2---7---0---0----2----4----6-
E  ----0---0---0---X----0----2----4-

In the transition from verse to verse and chorus to verse play the transition (TRANS) which is  
E1 - B - A - E and then  C#m - B - A - E   (one complete TRANS)

Listen to the song to figure out the strumming pattern, it's not that hard to pickup.  

Verse1

      E1   B        A                    E
Flow gently, sweet Afton, among thy green braes,
      C#m   B        A                    E
Flow gently, I'll sing thee a song in thy praise;
      E1   B        A                    E
My Mary's asleep by thy murmuring stream,
      C#m   B        A                    E
Flow gently, sweet Afton, disturb not her dream.


TRANS 1x


Verse2

      E1   B        A                    E
Thou stock-dove whose echo resounds thro' the glen,
      C#m   B        A                    E
Ye wild whistling blackbirds in yon thorny den,
      E1   B        A                    E
Thou green-crested lapwing, thy screaming forebear,
      C#m   B        A                    E
I charge you disturb not my slumbering fair.


Chorus1

     C#m  B               A      E
How lofty, sweet Afton, thy neighboring hills,
      F#m                    F#m          A              B
Far mark'd with the courses of clear winding rills,
     G#m  A        G#m     C#m  B   A   E     
There daily I wander as noon rises high, oooh,
      F#m                    F#m          A              B
My flocks and my Mary's sweet cot in my eye.


TRANS 2x


Verse3

      E1   B        A                    E
How pleasant thy banks and green valleys below,
      C#m   B        A                    E
Where wild in the woodlands the primroses blow;
      E1   B        A                    E
There oft as mild Ev'ning weeps over the lea
      C#m   B        A                    E
The sweet scented birk shades my Mary and me.


Chorus2

     C#m  B               A      E
Thy crystal stream, Afton, how lovely it glides,
      F#m                    F#m          A              B
And winds by the cot where my Mary resides,
     G#m          A               G#m         C#m    B
How wanton thy waters her snowy feet lave,
      F#m                    F#m          A              B
As gathering sweet flow'rets she stems thy clear wave.


Verse4

      E1   B        A                    E
Flow gently, sweet Afton, among thy green braes, 
      C#m   B        A                    E
Flow gently, sweet river, the theme of my lays, 
      E1   B        A                    E
My Mary's asleep by thy murmuring stream,
      C#m   B        A              B          E
Flow gently, sweet Afton, disturb not her dream.


To the end the song, play the TRANS through 1x and end on either E or E1... you choose 
which one sounds better.