Something along these lines perhaps?

knoppix@Microknoppix:~$ perl -Mstrict -wE '
> open my $inFH, q{<}, \ <<EOD or die $!; 
> foo  r1.1   abc
> foo  r10.1  pqr
> qux  r2.1   lmn
> bar  r33.1  xpq
> EOD
> 
> printf qq{%-6s%-4s%-s\n}, ( split )[ 1, 0, 2 ]
>    for <$inFH>;'
r1.1  foo abc
r10.1 foo pqr
r2.1  qux lmn
r33.1 bar xpq
knoppix@Microknoppix:~$
[download]

You would need to tweak this a bit for extra fields and might have to take the approach of generating the printf format progammatically.