To get a little more subjective, aside from wishing the weight cops wouldn't chime in to every thread, a person's knowledge of vehicles/mechanics and the ability to understand or affect the outcome of an "issue" plays a large part in their perception of an "issue" and also the difficulty in getting it resolved.
For instance, you said "rear main seal" cracked once and is cracked again? To me rear main seal is the rear crank seal on the engine, but I believe you were referring to the trans, or are you actually referring to the rear output seal on the transfer case.
From top to bottom, the first is pretty much major surgery to get to the rear main engine seal, the second is much less intrusive and cheaper to fix and the last is less than an hour and a $30 seal. I've replaced 2 of them on my 07 and countless others on many different vehicles.
If that is the transmission issue, it's not a big fundamental transmission problem, but rather more of an inconvenience.
Front end? Pretty much bulletproof save for a couple odd cases of early unit bearing failure. An alignment issue, short of a very rare yet possible bent axle (presuming 4wd here), are 99% of the time the result of a poorly aligned front end, bast caster adjustments or purely driving habits. (A diesel or any vehicle will eat soft tires if driven primarily on high speed curvy roads even with a good alignment and frequent tire rotations are necessary or your not getting max life out of the tires)
Whistling noise? IDK, cant help you there, but I'd be poking around the fire wall and the door seals. Only a few places where air could "whistle" into the cab.
How many miles on the truck?
