Ok, so here's a sample of what I have:

Code:

# Big table
Feature      100-0%    90-10%    80-20%    70-30%    60-40%    50-50%    40-60%    30-70%    20-80%    10-90%    0-100%
cdmass       12.010    10.809    9.6080    8.4070    7.2060    6.0050    4.8040    3.6030    2.4020    1.2010    0.0000
hdmass       1.0080    0.9072    0.8064    0.7056    0.6048    0.5040    0.4032    0.3024    0.2016    0.1008    0.0000
cdradius     0.8780    0.7902    0.7024    0.6146    0.5268    0.4390    0.3512    0.2634    0.1756    0.0878    0.0000
hdradius     0.1350    0.1215    0.1080    0.0945    0.0810    0.0675    0.0540    0.0405    0.0270    0.0135    0.0000

This is the first 5 lines of the master table, as a simple text file edited with vim. Each column has values for that particular percentage combination: the first one for 100-0, the second for 90-10 and so on. There are another 50 or so lines after that with more values of different features at that percentage combination.
My output looks like this:

Code:

# Modifications to force field
MASS
cd 12.01        0.878                                       Carbon
hd 1.008        0.135                                       Hydrogen 
hm 1.008        0.135                                       Other Hydrogen

In particular, this is the 100-0 combination. The format of the output is fixed: this is the way it has to be in order to be read by the program I'm using. There are another 40 or so lines after that for the remaining features and parameters.
In the third line, starting with cd, there are two values which vary in each percentage combination. The script needs to read the value from the table and write it in the correct column. For example, to prepare the 90-10 output file, I want it to read the third column on the third line (10.809) and write that down in the second column of the third line of the output file, then take the third column on the fifth line (0.7902) and write it on the third column of the third line of the output file. I want this to be repeated for every other parameter. I don't care if I need many lines to specify where everything goes, as long as it's automated. Is there a way to do this?
My first idea was to extract each column of the table in a temporary, intermediate file, then copy across from this to a blank output file, which has XXXXX instead of numbers, by giving a command to substitute the first XXXXX it finds with the first value of the column, then the second with the second and so on. What I don't know what to do is how to redirect the substitution from a file to another file.