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Thanks alister...

Another factor that might prove an important factor is which awk or which grep is used.
For example when using the same extended regex ^83 *(1[0-9][0-9][0-9]|2000)$
I got the...

That's a reasonable assumption, but it turns out to be incorrect (at least with the implementation I tested).

In my testing, the following code is over three times faster than the original...

The problem, really, is that you have a huge amount of data, not a slow program. How big are your records, really?

I haven't heard perl suggested to increase speed before. I don't think using an...

Performance not tested .. To avoid arithmetic calculations, try with egrep

$ egrep "83 (1...$|2000)" infile
83 1453
$

If the first value is fixed try:
awk '/^83 *[12][0-9][0-9][0-9]/{if($2>=1000 && $2<=2000){print}}' infile

You can give this a try:
#!/bin/bash

FILE="$1"

awk 'NR==1{print;next}!val{val=$NF;print ;next}{p=val;val=$NF;$NF= $NF-p}1' $FILE > newfile

Try this:
awk '{printf (/>/)?RS"%s"RS:"%s",$0}END{print x}' infile
your code does not work because of this: substr($0,1,1)

sed 'n;s/......//'

Test run with the data you provided in your latest post:
$ sed 'n;s/......//' MS_Pa-plex_1_tag1.sanfastq
@HWUSI-EAS656_0034:7:12:1:291#0/1...