Yes, each cylinder has it's own injector but the '88 2.9l uses Batch Fire fuel injection, on a V6 that would mean 3 injectors open at the same time, then the other 3 open at next firing.
This keeps intake full of fuel/air mix(like a carb did) so a single misfire probably won't be fuel related.
But I run a can of Seafoam in the gas tank once a year to keep my '94 4.0l idle smoother, it is Batch Fire as well.
If you have a shake at cold idle I would try to ID if it is just one cylinder doing it.
Unhook one spark plug wire and start engine, if miss is worse turn off engine and move to next spark plug wire.
If shake doesn't get worse with one wire unhooked then there is just one cylinder causing this.
A vacuum leak between intake and head near that 1 cylinder can cause it to have a lean mix and misfire when cold, and then as engine/metal heats up it expands, restricting the amount of air coming in and leak has less of an effect.
A worn out valve guide seal can add a bit of oil to a cylinder's fuel/air mix, this makes the mix harder to ignite, especially when cold.
Oil burning in cylinders can be seen on the spark plug tips, pull all spark plugs and keep track of which cylinders they came from, then look at them side by side and see what they tell you about how the cylinders are running.
Google: spark plug condition
On a cold engine compression is what allows an engine to start.
A spark will not ignite a fuel/air mix at any temperature, contrary to what you may have seen in Hollywood movies, lol.
The compression heats up the fuel/air mix so a spark can ignite it, once cylinder warms up then compression is not as critical, so a lower compression cylinder would "fire" normally once engine heats up.
A compression test on all cylinders may ID an issue
All spark plugs removed
Throttle plate open, hold gas pedal down all the way, this also cuts off fuel injectors
Compression meter in one cylinder
Crank engine until you hear 4 "hits", compression strokes in that one cylinder
Write down results and cylinder number
Repeat for all cylinders
What you are looking for is, at most, a 10% difference in all cylinders, usual compression is in the 150-180psi range.
When a cylinder is below 110psi if would be iffy to get it to fire cold.
Spark plug gaps are important but are set for longest life on untuned engine.
Larger gap will create a stronger spark, this is better for cold starts and low RPM operation but not as good for high RPM operation.
Smaller gap is a weaker spark but will give better high RPM performance.
The Factory recommended gap can be adjusted up to 0.01 in either direction for your driving habits

Or to help with a cylinder misfire issue.
Factory spec for the 2.9l is 0.044 gap
If you can ID which cylinder is causing the misfire try a gap of 0.50 and then 0.054 if that doesn't help.
A larger gap can allow firing at lower compression and with a little oil added.
But you will have to remember to regap or replace that plug every few months
Good read here on the 2.9l engines:
http://www.therangerstation.com/tech_library/2_9_Page.shtml