Following would replace each number in the entire file with an incrementing number starting from two.
let i=2|g/\v\d+$/s//\=i/|let i=i+1
Output
r2
...
r3
...
r4
...
Breakdown
let i=2 : Initializes variable i to 2
g/\v\d+$/ : a global command to search for numbers at the end of lines
s//\=i/ : a substitute command to replace the search matches with
the contents of i
let i=i+1 : increment i for the next match
All that's left to do is incorporate the commands to pad with zero's:
Vim: padding out lines with a character