hmm..let me see..try a few of these things im not sure they will work but its a start in the right direction of something simple going very wrong.
-Reset the ECU by disconecting negative side of battery, leave off for 30 mins
-get the transmission flushed and try Royal Purple ATF, use royal purple for engine oil as well. best stuff to use imo.
-get a timing test done on it. can get this by visiting your local autozone or O'Rielys parts store. or if u have a gun to do it with, do it yourself
-check your glow plugs make sure all are firing correctly
-turn the ignition key over but do not start.......any codes ?
-make sure all your sensors are functioning properly. you can do this by using hot/cold water for stall starts.
-Replace fuel filter
-Put " heat " into your gas tank, removes trash and water deposits. can be purchased at any parts store.
run through this list and if u still have the same problems, u will be able to tell the tech that none of these are the problem ( dealerships will bend you over for the small stuff ) so try and do most of them yourself while you can.
As far as the tuner goes...the tuner can be the reasoning for the Slipping but the surging im not exactly sure. the tuner you are using does not have a way to tune the tranny, just the motor and depending on which setting you use it at. the higher the setting, the harsher it is on the tranny. and if possible. try returning all settings to a little below average.
-Hope this helps you. Goodluck with the truck man