A/C sys transition box on wet ground

My house is making me sick. I believe the problem comes though the air conditioning system. When it rains or the ground is wet, I am much worse. The a/c unit is outside on pad. The transition box to the under house metal ducts is on the ground, actually it extends into the ground 5-6 inches. There are gaps in the box seams. There is 3 inch gap into box at ground level. We are on a lake.  I smell something most of the time, worse when dampness or rain.  I am asking A/C people to take the box apart, check for leaks, and get the box off the ground.  (note that orig house burned and when smelled smoke at floor vents, found gaps in metal work around vents which are now sealed and I assume that metal work to/from outside unit may have gaps too).    The A/C People are giving me the razzle dazzle routine.  I must solve this problem or move.  Questions:  Does this seem like a possible cause of my breathing problems?  Shouldn't the transition box be off the wet ground?  Sealed?  How difficult can it be to remove the metal around the in/out ducts, seal, and replace with space or pad underneath?