My daughter was diagnosed w/ allergies & asthma (at that time restricted airways) when she around 7 or 8 months. She is now 4, the dr. had put her on all kinds of different meds, at one point not too long ago singulair. She did have ill effect of singulair, (emotional issues, crankiness, unexplained crying, etc.) so we took her off of it. She had been taking zyrtec along w/ the singulair...and now just takes the zyrtec.
You are probably right about the cough that sounds like croup being from the asthma, that is how my daughter would sound also, (not everytime but sometimes) when she had any kind of a cough we did breathing treatments, with albutorol and pulmicort. That in time always helped open up her air passages, and helped w/ the coughing.
The trick is getting your child on the correct medications, which can sometimes be tricky. I would guess as with my daughter his allergies may be triggering the asthma, I hope that you can find relief for your little guy, it can be very frustrating. I am sure you are aware that asthma is a VERY serious thing, and not to be taken lightly. Hope you guys can get it under control soon! If you want to talk, or have any other questions that I might be able to help w/ don't hesitate to contact me. :)