Here are a few suggestions and questions:
"I have flow data from a nearby USGS rain guage, obtained from FEMA's FIS study. "
If you have the flood study ( the report, not just the FIRmaps) check to make sure you are using the same flows as were used in the study.
If you can, get the HEC-II or HEC-RAS data from FEMA's contractor. This may cost a little money but will allow you to see if you can duplicate FEMA's work.
Plot your field surveyed cross sections. Make sure they don't cross each other. Especially, make sure they extend far enough to the right and left overbank areas to include ALL of the floodplain.
Check areas both upstream and downstream from your project boundaries . Are there bridges, culverts, weirs or other structures present ? If so, these may control the starting water surface elevations for your model.
What did you use for a starting water surface elevation ?
Obvious, but make sure your cross sections are based on the same datum as the Flood Study. If possible, use the same bench marks as were used for the study. These may be found in the FIS report.
If you imported HEC-II data into HEC-RAS, make sure you got all the culverts and bridges. These can be lost when importing.
Make sure you are using the same Manning's "n" values as were used in the FEMA study. Even if you don't agree with FEMA's numbers, you need to make sure your work and FEMA's agree.
Also obvious, but check to be certain there are no major changes in the flood plain since the FEMA Srudy was done. Some of these studies are decades old.
Finally, why are you doing this ?
good luck