Seems like a short when I hook up neg. batt. cable.

You will have to take it to the Dealer. You may have burnt out or the "Control Module" needs to be replaced or reprogrammed. Make sure the battery has not reversed polarity also.

Locate the Positive cable marked with a + sign.. connect the red cable on the charger to this post.. Take the other clamp from the Batt charger and connect it to the neg Cable post Marked - or connect the negative clamp to anymetal part on the engine.

you have a dead short eather a pinched posative wire or you have a negative wire or a bracket toutching a posative hook up the neg. cable take a test light hook one end to the batt. the other end to the cable if shorted light will light start unpluging plugs and wiggleing wires till the light gos off and that should point you to the cause, make shore all lights and egnishion switch are off underhood light also.

a short most likley in the alternater have someone check the hot post on it for ground with the cable off there should be none

take a good battery from another car that you absolutely know is good. Try to prime the motor twice turn the ignition to start position...do not crank turn ignition off turn ignition to start position and try to start

hook them up in parallel, pos to pos, neg to neg from one battery to another, then pos cable to battery prs and ground cable to neg battery

has car been in a damp, wet or coastal enviroment for any length of time,may be electrical ground issues, make sure you have a good engine to body ground strap,turn everything off in car,put your hands around the pos and neg batt. cables,have a friend turn the motor over for 5sec, if either cable gets warm, replace it, if the neg gets worm, hook a jumper cable from batt. to engine block, try again, good luck

the dome light is draining the batt.
pull neg batt cable off when truck is running to see if the alternator is working correctly. check that glove box, hood,trunk/cargo light is shutting off when they should be.

seems to me you neglected to reinstall the ground cable body (to the eng.) possibly?
What did the 'new' engine come out of?
I hope you bought the alternators from auto zone or something and are getting them replaced under the lifetime warranty...

This is what I would do... remove the battery cable from the battery after you shut of everything in the car... lights blower fan et al... and see if you are getting an arc when you reattach it. That will give you a clue to whether a dead short is involved (if it arcs strong ) .
if you only get a spark it is normal , as there are draws that you can't dislocate w/o removing fuses.
If you dont get the dead short arc , then put a lead on the - NEG. post and ground the neg. to the engine dirrectly from the battery to any bolt on the engine bigger than 10mm. ( a bracket or the instilation hooks on the eng. should give you a reliable ground. if that causes an arc while the car is running my first thought is correct.
The lack of a good solid ground to the engine will cause the stalling out due to the numerous electrical componants that do thier job via variations in voltage. This voltage is measured in very small incriments,
and any deviation from set limits will cause your engine to run poorly.
It is my assumption that your battery starts the car , then the sole source of electric is being drawn from the altenater .
My ¢.02