Big 3 for misfires
Hard to get to or not you need to pull out 1 spark plug from each cylinder, keep track/label which plug came from which cylinder.
Compare them side by side and see if the tips tell you any thing, i,e, lean/rich, oily, etc......
With the 4 spark plugs out do a compression test.
Compression can't be intermittent so once tested and compared it can be taken off the table as possible cause of misfires.
But if it shows a problem this test will save you hours of pointless troubleshooting and $$ if you start throwing parts at the problem.
'99 2.5l has 9.1:1 compression ratio, so expected psi would be 165-175
Ford injectors should show 11-16ohms but since you are not getting Lean or Rich codes fuel is probably not the issue.
But do a live scan and after engine warms up watch the short term fuel trims(STFT)
A "-" number means computer is adding less fuel
A "+" number means computer is adding more fuel
The numbers should be jumping between +4 to +10 at idle(idle is suppose to be rich)
At higher rpm you should see -5 to +5
If you are seeing +10 to +18 then computer is having to add more fuel than expected.
There can be three reasons for this, lower than normal fuel pressure, dirty MAF sensor, or a vacuum leak.
MAF(mass air flow) sensor sets the "0" for the fuel trim, the amount of air coming in determines the amount of fuel to add to get the 14:1 air:fuel ratio, so dirty MAF will under report air volume, this changes "0" so computer has to add more fuel than it expects to because there is more air than being reported.
You can test fuel pressure with a gauge, 65psi is expected on a '99.
Vacuum leak can harder to find.
After engine is warmed up, unplug the IAC(idle air control) Valve, engine idle should drop to 500 or engine may even stall, either means no vacuum leak.
If idle stays high then start removing vacuum lines from intake and plugging the hole with your finger, when RPMs drop that hose has the leak.
Vacuum leak cause the same issue as dirty MAF, there is more air coming in than expected.
Just to add a little about the spark system
Ford uses a Waste spark setup, this means each cylinder gets spark on the power stroke(normal) and then again on the exhaust stroke(waste).
With the dual spark plug setup that means each cylinder gets 4 sparks per 4-stroke cycle.
When starting only the exhaust side spark plugs are working, once started all spark plugs are firing.
Once started you can unplug one coil pack and see if engine starts missing, that would mean the working coil pack probably has a failing coil.
Test other coil pack as well.
Last edited by RonD; 01-19-2015 at 01:16 PM.