Well to some degree you are in luck. People soft delivers some app engine programs for mass salary increases. I've been evaluating the process to determine if it will work for our purposes in annual salary increases. From what I've seen with a very superficial look, the mass salary increase executes in 3 steps. Step 1 builds a list of individuals to give raises to, step 2 reports the result of that list, and finally step 3 inserts new job rows for these people using the component interface for job data. Obviously, you will want to take a closer look at the final part (HR_SP_CI). Though I doubt that this app engine program will be your final answer, it should be a nice example of the proper technique to use.
To find where to run this process, go to Administer Workforce, Plan Salaries, Process, Update by Sal Plan/Paygroup. Don't get stuck on the first step. Most of what is happening here is creating of a where clause based on group selections (which is defined under Manage Human Resources). There is also some functional level descriptions under Mass Salary Increases in People Books.
I would use your SQR to load a temp table, then clone HR_SP_CI and rewrite it to read the data from your temp table to insert the correct data into job data.
Hope this helps.
Rekclaw