Yeah, i had a lot of what you're describing, pretty much symptoms similar to acute bronchitis, back when i smoked. I switched to vaping-only on a DBV also about half a year ago, and i feel heaps better now, but it did take a couple months for things to really clear up. And I was only smoking for about 6-7 years, a couple J's a day or so, so you might need even longer. Give it some more time.
As others have said, look into water filtration it GREATLY reduces the already reduced harshness of whip hits, as well as the fact that any bits that get sucked through the screen will get filtered out by the water. If i take a medium to large hit straight from the whip I almost always cough afterwards. I can take huge rip through water though and not cough at all most of the time though, so much smoother and moister and cooler (esp if you have ice in there too).
Here's where you can find the water adapters, which replace the mouthpiece on your hose (4th item down):
http://www.silversurfervap.com/Other_Parts.htm
If you don't already have a glass piece with a ground glass connection of those sizes, I can suggest a few very reasonably priced ones (I realize that ppl who are into thick and custom glass will shiver at some of the suggestions, but i'm trying to keep it reasonably priced and functional here, not top-of-the-line):
http://www.grasscity.com/double-bubbler-bong-2-0-with-shower-head-diffuser.html
(new version of a bubbler from Weedstar, which will take one of thoer 18.8mm (aka 19mm) water adapters perfectly. It has a removable showerhead diffuser, which looks really sweet (search youtube milkshots of it)... these have been selling like mad on grasscity because every time they get some in stock they're out of stock again within days.)
http://www.etsy.com/shop/dethstar
(A glass blower in the US with some nice looking and nicely priced bubblers, most seem to take 14.5mm adapters. Send him a message and see if he has any special deals. A bit pricier than the other options, but thats expected when you buy hand blown american glass, should have better durability, which could be a real + if youre a clumsy person)
http://www.grasscity.com/percolator-bong-blue-black-leaf-3.html
(just a cheap bong with a perc and some sort of diffusion on the downstem as well as ice fingers. I have a diff model black leaf bong currently, and while i have some issues with the massive size of it, it is of acceptable quality construction)
http://www.everyonedoesit.com/onlin..._Bong_Hexagon_Foot__250ml.cfm?iProductID=5909
(a nice small-ish bong from a well respected german glass company, with ice fingers but no diffusion on the downstem, but you could replace it with a diffused one as long as the size is right)
Those are just a couple suggestions to get ya started! I would definitely look for something small, not much more than a foot or so tall. I have a 2ft tube and its sometimes hard to get it filled and cleared in one breath because of how much sheer volume there is between it and the hose running into it.
*edit*
and when you're cleaning your wand out i hope youre saving the stuff you get out, because this "debris" is called wandhash and its very potent usually! Try smooshing some on top of a bowl next time you vape