P1000 code appeared. just replaced alt. recharged batt. wont start.

P1000 is a manufacturer specific fault code:

Ford P1000: OBDII Monitor Testing Not Complete.
Jaguar P1000: Engine control module (ECM) - internal error.
Kia P1000: System diagnosis incomplete.
Land Rover P1000: Engine control module (ECM) memory erased - no codes stored.
Mazda P1000: OBDII Drive Cycle Malfunction.

So depending on the manufacturer of your car would depend on the meaning of a P1000 code!

Did you have the charging system diagnosed or did you just guess at it being the alternator . The charging system is computer controlled . The starter isn't working because low power , battery dead . Is there B+ voltage at the wire on the back of the alternator .B+ voltage at pin 3 at the connector pluged into the alternator .
Charge the battery use a volt meter an test for B+ voltage at the places i mention . No check engine light ? DTC'S - diagnostic trouble codes stored .
Ford Smart Charge System Alternator Not Charging
Ford PCM controlled alternator testing

There is a fuse or fuseable link between the alt and battery, and the alt gets a signal from the key to activate the voltage regulator.
I would check for batt voltage at the alternator and you may need a wiring diagram to check for key voltage.

check ignition module, you may have fried it, if motor turns over the solenoid is o.k. -- your probably not getting any fire to the plugs, check to see if you are getting any spark at plugs

Sounds like the computer is in lock down. My sister has a 99 cavalier and used a cut key to start her car and a couple days later the car would not start. Tried everything then had to get a gm computer to reset the ecu. I have heard about the anti theft systems in GM cars that can cause this as well. Look into it if you cant figure anything out. There might be a code to input into the radio to take it off as well.

sounds like an alternater problem. the batt is not charging and is only running off the batt untill it runs out. check the wires ect on the alt and if that doesnt work, get a salvaged alt.

replace power wire from batt to starter

your charging system is not working,so your car is working only on batt. power,when batt.gets weak car will cut off! good chance alter nator is defective! check alt.elect. connections at alt,if con.are good its alt.

Cables from alt to battery can be deposited/burned/oxidized. In this case battery wont get charged. Also check the alternator connections. Cable might be burned or not tight enough
Also serpentine belt might be not tight enough
Good Luck

actually the only thing i can recomend is to have the alternator replace again for warranty and before starting the truck charge the batteries very well with a baterie charger make sure to charge them individually because with a low batterie the alternator has to put a lot of load and might burnt again
specially with dual batterie.