I decompile most with JPEXS, but JPEXS misses embedded assets, so I get those with Trillix. In some rare cases, JPEXS produces broken code (EquipmentToolTip has variable initializations in cases it shouldn't), in which case I use AS3Sorc's version.
For compiling, that's personal preference. For the Flex version, I am pretty confident that prod uses flex version 4.6.0.23201, so if you want it the most "prodlike" you can use that version, however I compile my client with a newer version, flex 4.16 + air 26, and everything works fine.