They are not in the game. I think the "incindiary gun" that you are refering to is really the "pulse rifle". I have seen a picture of it prior to HL2 release and "flare gun" or "incendiary gun" were the names given to them even though facts were not know. The pulse rifle is just a more powerful...
You can take out just one of the combine gunships and then position yourself in such a way to shield yourself from the other gunship while sucking plasma balls and banging away at the shielding on the portal. This gives you more time to destroy the portal before Breen escapes.
The only way is to run up the to top via whatever debri you can find and make your way back to the stairwell where you will find rockets galor!
Edit: In that second pic of yours you can see that fallen "I" beam, you have to run up that and then traverse across the frame work to the stairwell...
It would help alot if the subgun and the combine pulse rifle were more accurate at longer ranges. The Glock and the revolver are much more accurate than either of the above which is contrary to real life ( at least as far as the subgun goes). There seems to be some unwritten rule in the game...
As far as them trying to radio ahead is concerned, that bothered me too at first. But then I just chalked it up to Valve just trying to save space and time instead of coming up with a dialogue between the two radio operators it was just assumed that as soon as you walked out of the door they...