Gnuplot's using is meant to read data from a single file/stream so you need to merge the two files somehow. I would use python
for this since it is my go-to tool for just about everything. I would write a script which reads from the 2 files and writes the data to standard output. Something like:
#merge.py
import sys
file1,scale_factor_file = sys.argv[1:]
#Read the scale factors into a dictionary
d = {}
with open(scale_factor_file) as sf:
for line in sf:
key,scale_factor = line.split()
d[key] = float(scale_factor)
#Now open the other file, scaling as we go:
with open(file1) as fin:
for line in fin:
key,value = line.split()
print key,float(value)/d.get(key,1.0)
Now you can use gnuplot's ability to read from pipes to plot your data:
plot '< python merge.py datafile file_with_scale_factors' using 2