I've been running ROMS successfully with a 1km rectangular grid along the central east Florida shelf.  I'm focusing on summer time cold water upwelling so I'm starting on January 1st and running through October 31st; a ~150 day spin up period before comparing to in situ data.  I'm using NAM for surface bulk fluxes and RTOFS at my N, S and E boundaries.
ROMS has been hindcasting cold water upwellings and velocities within my grid are reasonable.  I'm now looking for options to further fine tune my input file and/or CPP header file, but I'm unsure of things to try.  I don't want to just change stuff and see what happens.
I've attached my choice of LBCs.  My main flow forcing is the Gulf Stream input daily to the south boundary from RTOFS.  I don't understand how users have set their nudging time scales and based on what information.  I'm updating my LBCs daily and no climatology.  I've seen mention of inflow and outflow time scales that people have used but I don't know how they are setting the input file to use them.
   LBC(isFsur) ==   Clo     Cha     Cha     Cha            ! free-surface
   LBC(isUbar) ==   Clo     Fla     Fla     Fla            ! 2D U-momentum
   LBC(isVbar) ==   Clo     Fla     Fla     Fla            ! 2D V-momentum
   LBC(isUvel) ==   Clo     RadNud  Rad     Rad            ! 3D U-momentum
   LBC(isVvel) ==   Clo     RadNud  Rad     Rad            ! 3D V-momentum
   LBC(isMtke) ==   Clo     Gra     Gra     Gra            ! mixing TKE
   LBC(isTvar) ==   Clo     RadNud  RadNud  RadNud \       ! temperature
                    Clo     RadNud  RadNud  RadNud         ! salinity
      TNUDG == 2*0.0d0                     ! days
      ZNUDG == 0.0d0                       ! days
      M2NUDG == 0.0d0                      ! days
      M3NUDG == 0.0d0                      ! days
      OBCFAC == 2.0d0                      ! nondimensional
I've included a section of my *.h file.  My only idea with my CPP file is to try GLS mixing.  
#define UV_C4VADVECTION
#define UV_VIS2
#define MIX_S_UV
#define TS_U3ADVECTION
#define TS_SADVECTION
#define TS_DIF2
#define MIX_S_TS
#define MY25_MIXING
#define KANTHA_CLAYSON
#define N2S2_HORAVG
Thank you for suggestions or referrals to detailed information for my questions.
Chris Flanary
cflanary@my.fit.edu