We have a 4" and 6" groundwater recovery pipe header that is approximately 3000ft long.  Historically, 15% HCL mixture has been pumped through the pipe in 5000 gallons shots to loosen the scale.  The pipes are Fiberglass and now require additional treatment.  We are considering switching gears to a citric acid, starting with 50% solution and diluting as needed.  Any recommendations?  The scale is primarily iron scale and some limestone/calcification/mineralization.
 

I once had to passivate a 22,000 gallon stainless steel rail car using citric acid.
We had to use hot water (160-F) to get the citric acid to dissolve.
But the actual passivation job went great.
When the job was finished, we pumped the spent liquid into an old old FRP tank.
The environmental folks would not allow disposal of the spent through the plant discharge systems.
Managers looked at the cost and wanted to save the spent for reuse.
Five years later I left the company.
No reuse opportunity ever occurred.
The spent material was still being stored in the FRP tank.
Following a State audit, environmetal folks were trying to explain why the 22,000 gallons was not Hazardous Waste.
Good Luck to You

Both acids will work decidedly better if there is wetting agent, dispersant, and rinse aid are added to acids. If you have the acids you should be able to buy an additive package. Your best approach is to add the acid circulating if possible and at intervals stop the flow and let the mixture sit for 15 minutes and resume circulation. If you have to go with slug flow pump the acid in at intervals to allow longer contact.

As you state this is aground water application is there any petroleum products in the fluid.