OK. Each file contains 10 to 15 records and out of those 15 records you want to select 1000??????
10K usually means 10,000 or 10,240; I have no idea what 10L means.
And, if a sample file contains ~1,000 lines and the total file size is 1,000 characters; each line consists entirely of a <newline> line terminator and there is no data to compare??????
Please show us some data with actual values similar to what would appear in your files and the actual results that should be produced from that sample data. If we can't see data that we can feed into scripts that might do what you are trying to do so we can see if the code we're suggesting produces the results you are trying to produce, you are asking us to write code with both hands tied behind our backs. I have absolutely no idea from the above how we are supposed to determine what you consider to be a mismatched record.

With what you have told us, the only thing I can suggest is to use the diff utility to compare pairs of files.