If you create a tab-delimited file from your first table, you can use the following R code to create a tab-delimited result file that looks like your second table:

library("GenomicRanges")
library("IRanges")

datadir="/your/data/dir/"
setwd(datadir)

#Import regions to exclude
Data2Mergefile="Data2Merge.txt"
Data2Merge=read.table(file=Data2Mergefile, sep="\t", header=TRUE)

#Create GenomicRanges object for manipulation
ranges2merge = GRanges(seqnames = Rle(Data2Merge[,"Id"]),
ranges = IRanges(Data2Merge[,"start position"], end = Data2Merge[,"End position"]), 
strand = Rle(strand("*"), length(rownames(Data2Merge) ) ) )

#Simplify ranges to merge overlaps
reduced=reduce(ranges2merge)

#Reformat and print to file
results=data.frame(Id=as.vector(seqnames(reduced)), Start=start(reduced), End=end(reduced))
write.table(results, file="merged.txt", sep="\t", row.names=FALSE, quote=FALSE)

EDIT - After OP's input file and comments.

First we will swap the start and end position, if start position is greater than end position and then we will sort this file.

Say this perl script is strand.pl -

use strict;
use warnings;
open my $file, '<',$ARGV[0] or die "Unable to open input file: $!";
my @data;

while (<$file>) {
@data = split;
  if ($data[1] > $data[2]) {

    my $temp = $data[1];
    $data[1] = $data[2];
    $data[2] = $temp;
  }

  print join("\t",@data),"\n";
}

Use -

perl strand.pl input.file |  sort -k1,1n -k2,2n > sorted.file

Now we will merge the overlapping positions.

Then use this perl script say merge.pl -

use strict;
use warnings;
open my $file, '<',$ARGV[0] or die "Unable to open input file: $!";
my @data;

while (<$file>) {

  if (not @data) {
    @data = split;
    next;
  }

  my @new = split;

  if ($new[0] == $data[0] and $new[1] <= $data[2] + 1) {

     if ($data[2] < $new[2]){
     $data[2] = $new[2];
      }
  }
  else {
    print join("\t", @data), "\n";
    @data = @new;
  }

  print join("\t", @data), "\n" if eof $file;

}

Use -

perl merge.pl sorted.file > result.file

if I understood your Question correctly: 1.Add hash to the header line.

2.check to see if start positions ($2) is less than End position($3):

you can do that simply by using awk:

awk ' BEGIN {OFS = FS = "\t"};{if($2 < $3)print ; else print $1, $3, $2}'