$ perl -wle'
    my %neg = ( o => "i", i => "o" );

    while (<>) {
        chomp;
        s/([io])(M*)(\.+)/ $1.$2.( $neg{$1} x length($3) ) /eg;
        s/(\.+)(?=M*([io]))/ $neg{$2} x length($1) /eg;
        print;
    }
'
....MMMMiiii
....MMMMoooo
iiiiMMMM....
ooooMMMM....

ooooMMMMiiii
iiiiMMMMoooo
iiiiMMMMoooo
ooooMMMMiiii