1.ok am also designing the airborne antenna which is made up of the rectangular waveguides....
2. may be i can help u
there are numerous ways to make the rectangular waveguides in HFSS,few of them are;
A) just draw a rectangular box and give it a material like pec or anything,and suggest where u have to feed it from...normally they are feeded from the front face of the waveguide where a(width) and b(height) is located..just right click on that face,choose assign excitation,then choose waveport,now in the waveport window click on modes.here u can see the option of integration line below now give the intgration line from one edge to another...dont leave the line in b/w otherwise u ll get the error of invalid line
......NOTE:normally the intgration line doesnot have any effect,esp. in my case so u can ignore it...but for lumped ports it is necessary
B)u can also draw the wguide by making 2 boxes (one having large dimensions of X,Y,Z and one having less)and subtracting the one with small XYZ from the large XYZ..so a vacum will automatically be created ...now put a lumped port with the same method of intgration line on the front side.
3)dont forget to make radiation boundary at lambda/4 on each axis(if working in far field)
4)by the way wat are u trying to make at the end of your project????