1999 jeep wrangler 2.5l wont start and beeps.

Take your fob to a parts house and they have a fob tester to make sure it is not the fob.

Probably a bad key

did you RTM read the operators guide yet,
it tells you why all beeps beep and what lamps flash, (warning) and why. did you?
you turn on, the head lights, (what about 1st click , parking lights"?)
and does the dash cluster, show warnings of any kind?

if a door is ajar the system will think, you are exiting veh. with lights on and tell you, buy beeping ,etc.
but on my jeep it says on the dash DOOR, or on EVICs, (not yours)
the newer car even tells what door IS AJAR.
mine on shows , "DOOR"
the operator guide will say, check all doors for ajar, and get warning clear before driving....etc.

if you lost the guide here it is for free

http://justgivemethedamnmanual.com/jeep/jeep-wrangler-owners-manuals/

click the 05 link
ignore beeps, there are just too many .. i look at the cluster and learn to read it..
my newer jeep 08 can produce 1000s of errors,,,,, possible.
in fact the intent it to beep to tell the driver to look at the cluster
for in depth, causes.
see chapter starting on page 136'

once sound it makes is Check gauges chime. so check them.
and headlamps left on
and door ajar.

page 63
NOTE: If the driver's door is left open, and the headlights
or parking lights are left on, the "High Beam
Indicator Light" will flash and a chime will sound.
Lights-On Reminder
If the headlights or parking lights are on after the ignition
is turned off, a chime will sound when the driver's door

its a crude system, and evolved to complex in 2007.
"DOOR" or RF-door , on mine.
or

NOTE: A tone will chime if the turn signals are left on
for more than 1 mile (2 km).

search manual for
"chime will sound"

The beeping alarm would be for leaving the key in the ignition or the lights on. Maybe a gauge that had dropped to zero.
Let us know if it happens again and what the conditions are.

Could also be a fuse or relay problem.
You'll need to find out if the coil has voltage and if the pick-up stator in the distributor is sending a signal to the computer.
Might want to check the computer for trouble codes too.

Double check that everything is reconnected properly

check the crank sensor

If we are talking about your radio, dial to the station you like then push and hold on the button you want until you hear a beep. The stion you like will be on the button you selected.

That's not a remote starter on your key chain, it's a keyless entry for an alarm system.

Checking your fuel pressure would be a starting point.