2000 Honda Civic Dx will not start, gas pump is ok, but not gatting spark to spark plugs, suspect the igniter or the coil can you help

How do you know it is not getting gas? Have you tested for fuel pressure? Does it have spark at the spark plugs? Have you checked for power to the fuel pump? Given that the engine has been replace make sure all the ground wires are attached and tight. I strongly suspect you have a loose ground wire somewhere.

They check the immobilizer system? Also ignition switches fail.

its most likely the distribuator igniter

It seems your ignition switch has burned out - verifying good starter operation was an important component in furthering your diagnosis effort. The ignition switch is really a relay separate from the ignition key cylinder - when it fails to send battery voltage to the starter motor, you'll have the no-start condition described.
See the Honda Ignition switch replacement illustration below.

Just for completeness' sake, here's the generic response of a mechanic to a vehicle's no-start condition:

Priority Action Part Type Cause
1 Inspect Ignition Switch - Improperly Connected or Faulty Ignition Switch.
2 Inspect Battery - Battery Discharged or Faulty.
3 Inspect Battery Cable - Coroded, Broken, Shorted or Poorly Connected Battery Cable.
4 Inspect Solenoid - Starter Solenoid Faulty.
5 Inspect Starter - Starter Motor Faulty.
6 Inspect Wireset - Worn or Damaged Spark Plug Wires.
7 Inspect Ignition Coil - Faulty Ignition Coil.
8 Inspect Distributor Cap - Loose, Cracked or Worn Distributor Cap.
9 Inspect Spark Plug - Incorrectly Gapped or Fouled Spark Plug(s).
10 Inspect Distributor Rotor - Loose, Cracked or Worn Distributor Rotor.
11 Inspect Fuel Tank - Fuel Tank Empty.
12 Inspect Carburetor - Worn, Faulty or Damaged Carburetor.
13 Inspect Fuel Pump - Faulty Fuel Pump.
14 Inspect Choke - Stuck or Improperly Functioning Choke.
15 Inspect Fuel Filter - Clogged or Dirty Fuel Filter.
16 Inspect Fuel Pump Relay - Faulty Fuel Pump Relay.
17 Inspect Fuel Injector Pressure Regulator - Faulty Fuel Injector Pressure Regulator.
18 Inspect Fuel Pump - Low Fuel Pressure.
19 Inspect Engine Control Computer - Incorrect Operating Information Being Delivered and Sent From The EEC.
20 Inspect Fuel Pump Strainer - Clogged or Dirty Fuel Pump Strainer.

Illustration courtesy honda-tech.com (from 1994 Honda Civic EX manual).

http://honda-tech.com/showthread.php?t=2577784

REPLACE DISTRIBUTOR CAP AND ROTOR.AND PLUGS WIRES.IF GETTING NO SPARK TO PLUGS.CHECK SEE IF IGNITION COIL GETTING POWER.IF NOT CHECK IGNITION FUSE.IF POWER GOING TO COIL.FAULT EITHER COIL IS OPEN OR FAULT IN THE IGNITION MODULE IN THE DISTRIBUTOR.

Test your coil pack on the distributor. sounds like problem. its the pack inside distributer cap screwed to distributor.

you should change the water pump so it wont do that no more

Try pounding on the gas tank with a rubber mallet or similar tool. (careful not to dent the tank) Try starting it. If it runs, replace the fuel pump (it's nfg). I've diagnosed numerous fuel pumps this way. Remember the pump needs to be replaced, if you drive it, you don't know when it'll fail for good. Hope this helps. Please post the results.

The Ignition Can Cause This Try Taking All The Keys Off Your Keyring And See If When You Use Strictly The Vehicle Key If It Still Does This.

Could be coil or ignition module starting to fail