Do it in a small steps. Test input/output and learn incremental:
1. Find all your chunks and learn their structure:

Code:

awk '/<pairwise.../, /<\/pairwise.../' INPUTFILE

2. It looks like you want process lines with only 3 fields, pipe the output to the next awk:

Code:

awk 'NF == 3'

Maybe it's not enough and you want something like

Code:

awk 'NF == 3 && $1 ~ /[0-9]/

or

Code:

... && $2 ~ /^[0-9.]+$/ && $3 ~ ...

3. You should get the even(!) number of lines. You can check it piping to "wc -l"
4. You can squeeze your lines with:

Code:

sed 'N; s/\n/ /'

5. And cut them with

Code:

cut -d' ' -f2,6

6. And then you can format your numbers with printf:

Code:

xargs printf "%.2f %.2f\n"

The final result:

Code:

awk '/<pairwise/, /<\/pairwise/' INPUTFILE | 
awk 'NF == 3' | 
sed 'N; s/\n/ /' | 
cut -d' ' -f2,6  | 
xargs printf "%.2f %.2f\n"

And one more time - you can change, tune, test every your step separately.