I have a 90 Samurai 1.3 EFI and it runs like it's running on 2 cylinders in the mornings until the high idle kicks in then runs smooth I have only owned this rig a couple months but here is a list of things I have done as well as some of the mod's that are on it to mabe help pin point a problem.

this last week I have
1. tune up (plugs,wires,cap & rotor)
2. new O2 sensor
3. oil change including cleaning K & N air filter
4. adjusted valves per FSM
5. ran Lucas fuel system cleaner in gas tank

some of the engine mod's
1. cold air intake
2.header with 2 in exhaust

Mine does the same thing, 1.6L Sidekick, could the injector
related spray pattern, as my engine is a resent rebuild so I
would doubt it is low compression, it also has no low sounding
starter noise when cranking, but I have not done a test

Wild

Check the EGR vavle.  If that is sticking it will cause a cylinder drop at idle. 

Thank guy's I'm going to vacuum check the EGR and do a compression check this weekend to see where I'm at with this zuker..it's been neglected to say the least but I'm bringing it back to life slowly but surely