2 New batteries installed fully charged & new alternator , alternator is not charging batteries , is there a regulator mounted elsewhere ? if so where is it. alternator gets hot to the touch in only a few minutes tester reads , its not working , the power is going some where but not to the batteries

You out the alternator in incorrectly. please triple check the installation of the alternator.

What model and make is your truck?
Older vehicles differ widely from later ones. Is the regulator separate from the alternator? If so, you might need to replace the regulator.
On some vehicles, the regulator was booted by the indicator lamp on the dash. If the light does not work (blown), the alternator does not charge.

Due to the nature of the battery technology used with vehicles the alternator is mostly incapable of charging the battery. The car alternator is designed to keep a fully charged battery fully charged and to provide all the power for the car equipment.

The alternator charge rate is regulated by a voltage regulator. Because the alternator output is connected to the battery, the alternator and battery voltage will be the same and the voltage regulator monitors that voltage.

The lower the battery voltage the more output the alternator will produce in order to correct the situation but because a lead acid battery has a high internal resistance to accepting a charge the terminal voltage will quickly rise to the alternator regulated voltage and fool the alternator into thinking the battery is fully charged when the output will drop to the order of just a couple of amps.

Switch on the headlights or a similar load that will lower the battery voltage and the alternator will increase it's output again - but only by the amount of current the headlamps or other load is consuming.
It matters not what the alternator rated maximum output is, it is designed to provide only the necessary current and no more.

The only time an alternator should ever need to produce maximum output is when on a dedicated testbed and then only for a short duration to avoid damaging the unit. Testing the current output on a modern vehicle is not recommended except for the regulated voltage testing and a rule-of-thumb output test where all equipment is switched on and the engine speed raised while the battery voltage is monitored.

Most modern alternators use an internal voltage regulator but a few systems use a separate voltage regulator. No alternator rebuild would be complete without a regulator test and probably a new or replacement regulator, which is where the majority of charging system problems are, or the brush gear.
Assuming the wiring is ok, no alternator should suffer any harm if the voltage regulator and auxilliary diodes (if fitted) are in good order though fitting a defective or a discharged battery can cause it to overheat and be damaged.

The alternator usually just about stops producing an output when the battery voltage is in the region of 14.5/14.8 volts.
Your description indicates the voltage regulator is not working correctly - unless 40 amps was being consumed by the car equipment the alternator should not have been producing 40 amps.. I suggest you also have your battery tested

sounds like a bad battery - check that -even if new try a well known used battery if you need to. Also charge the battery to full charge and then try it. Many ford [ merc] will tell you do not install a battery that is not fully charged as it will cause problems with the charging system. As a last resort try a new battery with a FULL CHARGE and check the wiring for very hard places near the alternator. These can be a sign of working the assembly too hard. Consider replacing the 'hard' portions of the wires.

If you have a fully charged battery when you installed then 14 volts is way to much charge for the battery which would mean that the alternator probably has a faulty regulator and the alternator needs to be changed otherwise you will continue to install new batteries. If the battery was in an uncharged state then it is possible for the alternator to charge at full capacity to charge up the battery.

your regulator is not keeping these other batteries fully charged.

Check/inspect quality/condition of cables between the alternator & the positive (+) post of the battery. Also check quality/condition of ground cables & straps between battery negative (-) post and chassis and to engine block. One final check is the alternator's regulator connection between it and the UH (underhood) junction box (fuse & relay box).

Make sure all connections at alternator are attached. On some, the regulator is inside the computer and if bad, requires computer change.

The alternator is not charging the battery. Could be alternator, voltage regulator (which is usually in the alternator) , dirty/loose connections. First I would inspect all relevant electrical connections, clean & tighten. If no change -- replace alternator.

But be sure to fully charge the battery before you run the new alternator (follow alternator installation instructions).

Check your Belt and see how tight it is. It may be Tight just not tight Enough to Fully Charge the Battery with the Alternator.