The experience with JRA-55 is awlful. I was stuck in this for a long time and finally found that some of the data is corupted...Anyway, here are some tips for using JRA-55. (JRA-55 is sucdessor of JRA-25, the latter is widely used in the literature. JRA-55 improves the assimilation strategies and also extends the period, from 25 years to 55 years, since1958, I think).

(1) Some features about JRA-55: There is no soil moisture and soil temperature in the dataset, while WRF need them to initialize the simulation; the vertical levels are 27 (1000,975,950,925,900,875,...250,235,100), but are different from the traditional level bins as used in other dataset, say FNL. be aware of this.

(2) Basically, we need presure (surface, sea level, upper air levels), air temperature (2m, upper air level) , u&v wind component (10, upper air level), RH (2m, upper air level), Height (upper air level), soil moisture (underground levels), soil temperature (under ground level), and constant variables (land mask, sea ice, snow depth and water equivalent snow). Three catergories: surface, vertical levels and constant.

Tip1:Use JRA for surface and vertical level data, and FNL for the other (soil moisture/T), by changing 'namelist.wps' for different source.

Tip2:DO NOT include any vertical data from FNL, otherwise you will get errors like "WRF_DEBUG: Warning DIM 4 , NAME num_metgrid_levels" (the error is just because you have different dimensions of your 3D variable). The way to avoid this is to modify Vtable (Vtable.GFS.YLO). I uploaded the one I used. The one for JRA is also attached in case (Vtable.JMGSM.YLO)

Tip3: Choose the same vertical levels for upper-air variables (TT,UU,VV, HGT&RH). Some of them have more than 27 levels.

Tip4: Use NCAR archive for the data (http://rda.ucar.edu/datasets/ds628.0/), since it takes days for JMA to process your application, you can try though.

Tip5: 'namelist.input' needs to modify. num_metgrid_levels = 28, e_vert= 29, 29, 29, with my sample attached also.

I run a heat wave case from 2010-07-01 00 till 2010-07-11 00. However, no matter how I try with different solutions or debugs, I got no RH from 0701 00 to 0702 06. The rest of them is ok. still can not figure out why....I start from 0702 in WRF simulation at last. It's still werid to me...Since JRA-55 is just updated and released to public, no such errors have been reported yet.

Good luck!