ford windstar misses when accelerating

my 1999 ford windstar misses when i accelerate or up a grade usually over 55 mph but not always. I have a code scanner and have the green light there. It seems as if it's an ignition problem i have changed most of those related parts recently and of course no engine light .As far as traveling down the road at any speed not heavy accelerating the vehicle works great. Could it be the the tranny it was replaced and has around 75000 mi on it ? or could it be a sensor causing the problem.Hope some one has some suggestions . WHOW what would we do without Automotive forums, Thanks>

The first thing that I would recommend is the routine maintenance things.....fuel filter, PCV valve.....fuel system cleaner (Berryman's B-12).
Verify that the vacuum line to the fuel pressure regulator is intact (they can work loose, crack, etc).

Also, verify that the IMRC shafts are connected to the electrical actuator for BOTH banks of cylinders. VERY common on the 1999 and newer (which have the single electrical actuator whereas the older 1996-1998 have 2 vacuum driven actuators).
These come unconnected....1 bank or even both banks and can cause issues similar to what you are having.
I am not leaning toward the transmission at this point.....much less likely, and there are more likely / easier / cheaper things to go for.

I know this is a month old, but if you're like me and put it off...

I just downloaded the Haynes manual and there is a very good troubleshooting section. I have a similar problem and the troubleshooting item that seems to best match what I'm experiencing is: "Hesitation or stumble during acceleration". I notice it most when climbing a hill, but it also happens around 40mph on flat land.

The advice for this is:

1) Ignition system not operating properly.
2) Dirty or clogged fuel inector(s).
3) Low fuel pressure.
5) Fuel injection or engine control systems malfunction.

There are several others that might match your particular scenario a little bit better. I would recommend purchasing or downloading the manual and giving the troubleshooting section a quick browse. It's very comprehensive.

I believe another source of this problem is clogged EGR ports in the lower intake. They are easily cleaned with removal of the upper intake, a vacuum cleaner, and a small drill bit.