For basic purposes, you have this right. If you changed angles at all, you would have to do some trig to get the vertical velocities of the emissions and such. There's probably something I'm missing, but screw physics right now, it's Christmas break!

The way I did the equation:
(Note: I used the values you specified for mass and the percentages. If those are wrong, the answer is obviously also wrong)

Using…
ParticlesPerMinute1 = 4500
ParticlesPerMinute2 = 4000
m1 = 9kg
m2 = 9kg
v1 = 18m/s
v1 = 20m/s
verticleForceEfficiency1 = 0.873
verticleForceEfficiency2 = 0.9362
m = 943.14kg

FNET = FEmission – W;
a = (FEmission – W) / m;

a = ((((particlesPerSecond1)(m1v1))verticleForceEfficiency1) + (((particlesPerSecond2)(m2v2))verticleForceEfficiency2) – (mg)) / m;

a = ((((4500/60)(9*18))0.873) + (((4000/60)(9*20))0.9362) – (943.14*19.82)) / 943.14;

a = 3.34m/s/s

Should note that the values you are using for the emission speeds should probably be an average between the MinVelocity and MaxVelocity.

This is only the y acceleration though. But that's all we really need I guess, just to know how much our rockets can actually hold up without having to mash the keys for the burst.

If you wanted the resultant acceleration (x and y components) then you'd have to do a bit more trig on that. I'm not going to walk through it, but if anyone ever needs it, PM me and I'll be glad to serve my hours of boredom to physics.

Another note... why are we doing this again?
Oh well, I'll just throw it in, why not.
The only accelerations you would really need are the ones for going to either side (gets same answer for each side, but one will be negative) and the accels for up and down (down will be different, there is gravity!). I can't imagine why you would ever need to find the acceleration at some obscure angle, unless you were trying to figure out what the greatest possible angle is that you can fly at without falling from the sky.

tl;dr

Excellent, I not worried about computing the trajectory of a missile, since that would be utterly useless, so I dont need to worry about any math other than taking off.

It is being done as a intellectual curiosity of mine, ie. So I can make some decent mods that arent over/under powered.

Thanks all.