I just replaced the alternator on my 91 Civic DX a couple of days ago after the battery light stayed on and although I haven't had any charging problems anymore I noticed that all the lights are pulsating at low rpm or when at a low speed (dash,head and interior lights) was wondering if anybody has seen this problem or could it be a bad alternator?

Sounds like the idle rpm is too low. See if this helps:

Honda Civic Idle Speed Adjustment

Idle speed adjustment is not straightforward. The idle adjusting screw is located on the end of the throttle body and is often “leaded in,” to prevent people from fiddling with it. Take a small screwdriver and dig it out. Also, locate the blue tachometer wire, which goes to the distributor. Actually, it is connected to the igniter inside the distributor. The tachometer wire is buried, with a protective rubber cover over it, in a cluster of wires near the clutch master cylinder reservoir. Take a small screwdriver and carefully pry the connector from the rubber cover, using the small hole provided for this purpose.

1. Start the engine and warm it up to normal operating temperature.
2. Turn engine off and connect the tachometer to the blue tachometer wire.
3. Disconnect the 2P connector from the Idle Air Control (IAC) valve.
4. Start the engine with the accelerator pedal slightly depressed. Stabilize the rpm at 1000, then slowly release the pedal until the engine idles.
5. Check idle in a no-load condition; i.e. headlights, blower fan, rear defogger, radiator fan, and air conditioning turned OFF. Adjust “Initial Idle Speed” to 450 rpm, by turning the idle adjusting screw.
6. Turn the ignition switch OFF.
7. Reconnect the 2P connector to the IAC valve, then remove BACK UP (7.5 A) fuse in the under-hood fuse/relay box for 10 seconds to reset the ECM. Make sure to record any radio codes first.
8. Restart and idle the engine in a no-load condition for one minute. Verify that the “Final Idle Speed” is around 700 rpm.