What I'm seeing as the problem is the longitudinal axis (front to back) is off, correct? It won't change, no matter what you put in for the numbers, right? If that's the case:
COPIED FROM THIS POSTOkay, the VERTICAL (up & down) is not useless, the LONGITUDINAL (backwards & forwards) axis is useless. Its controlled by the smoke file itself. If you open up the relevant smoke file, you will see a whole bunch of sections that probably don't make a lick of sense.
Don't worry about most of it. It isn't comprehensible to me, either. But if you want to make this work, we'll need a bit of patience.
First off, make a copy of the smoke file and change the name a little. It doesn't matter what the name is, just so long as you change the name in the aircraft config when you get done as well. That way, the smoke is still correct for whatever other aircraft uses it, and you have an edited version that allows you to use it on other aircraft.
When you open up the smoke file, there should be a first section titled [Library Effect]. This section is only relevant if we want to change how long the smoke stays active. Since all we want to is to control where it comes from, ignore the first section.
The section(s) we are looking for are titled [Emitter.*], where * is any number. There may be only one of these sections; there could be ten. It just depends on how complex the smoke system is. To edit the longitudinal axis, scroll down until you see a variable labled "Z Offset" (I'm almost certain this is the correct "Offset" section). Change this number if you want to edit the forwards and backwards distance. Negative moves backwards and positive moves forwards.
Now scroll down until you see the next [Emitter.*] section. Change the same variable, the same amount. If the two numbers (Z Offsets) do not match, change them by the same AMOUNT and do not make them the same number. Do this for all [Emitter.*] sections in the fx file, and it should make this work.
If this doesn't work, or you would like to learn more, check out the Special Effects SDK, which should tell you everything you ever needed to know about effect files (or just confuse the hell out of you).
Good Luck!