Merging two large scans

i am trying to merge a set of "two-sided" scans of roughly 100+ pages which i now have of a "front" and "back" side for. Basically I am going to have a pdf of each of these and I am going to keep the images in two folders as well.
aside from the fact that i will have to do a little culling where a scan added an extra bad page due to a bad feed or in making sure that the documents and/or images line up - is there a way to merge these two into one document that goes front-back-front-back etc like the original document?
i tried getting advice on how to get this hp 8500 all in one scanner to do the two sided scan on its own but my recollection was that I was unlikely to get this to work.
TIA for any advice.
Jon

Thank you.
I actually need the different margins to allow for 3-hole punch. This was created from an HTML file and scripts were written to give me the margin space that I need but each document had to be run just one way which is why I now have to merge the even/odd pages. Apparently there is a script that will do this.

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Connected to 192.168.1.36.
220 192.168.1.36 FTP server (tnftpd 20080929) ready.
Name (192.168.1.36:lydiachet): carolchet
331 User carolchet accepted, provide password.
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250 CWD command successful.
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229 Entering Extended Passive Mode (|||62595|)
150 Opening ASCII mode data connection for '/bin/ls'.
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drwxr-xr-x 12 carolchet staff 408 Jul 21 11:29 20120721-112923
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229 Entering Extended Passive Mode (|||62596|)
150 Opening ASCII mode data connection for '/bin/ls'.
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I have pasted the code below.
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package com.cisco.asit.icn.common.servlets;
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parthInfy wrote:
Hi there,
I am trying to merge two byte arrays into one byte array
and write into a new word document using OutputStream object.
But in the new word document that is created only the contents
of the first byte array are being shown and not that of the second one.
Because the end of the first byte array contains a "document ending" tag and anything after that is just flotsam. And, even if you could remove that "document ending" tag, there is for the second a "document begin" tag. (Among many other tags and flags in both documents.) Word (ar just about any) documents are not simple text files to be concatented, truncated, twisted, inverted, or whatever else, at your pleasure. You actually, God forbid, have to kinow what you're doing, to manipulate them at this level. And, surprise, surprise, you don't.
Edit: Google "POI"

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