Database Comparison and Filtering

Hello Everyone,
We have a issue and are hoping we will find some who can develop or recommend a system to help us resolve our problem.

We have values entered to our database constantly from a number of remote sites this is done via third party software which we do not have much control over. There is a column in the table which writes a Boolean value and because of a certain fault with the software there is a redundancy of values in the column.

What we are expecting the developer to help us with is to develop a application which will use the database in which the values are being entered from one server and compare it with the last record of another database we will be using for actual logging purposes on another server. The application must allow us not only to filter the values on this criteria but also allow us to make a few changes to columns and add a few columns more from a form based system. Each server has multiple databases and each database in turn has multiple tables. So we need a way to bring in the list from the server which is being entered from third party which also creates table names and then allow to create new tables in actual server if it does not exist.

It may be a bit confusing let me know if you will require any more clarifications. The databases being used are mysql and the server is linux.
Thanks and look forward to all your questions suggestions or replies.

Nelson