As far as going with a day cab or not to, it all depends on the truck and your prefrences. Some day cabs are very short and there is no room to even tilt the seat even slightly. In my case we left about a 1 1/2' of the sleeper on so it allows for the seats to be moved back or tilted to about a 45 degree angle. (Wife likes that) You are going to find more trucks with sleepers and pricing is usually a bit better on these than the day cabs. (Since there are more on the lots) As far as cost for trimming it down, again it depends on what your doing, but I would budget $3,000 - $5,000 if it is integral and much less if it is not.
A major factor to remember when selecting your dream truck and the configuration of your conversion. If you want a over the cab bunk, your cab can only be a certain height. There are many trucks out there that will not accomodate a over the cab bunk, becuase it will raise the overall height of the conversion beyond what is allowable 12'6" is about where you want to be.
As far as keeping the air ride cab or not. Eventually your rubber boot will degrade to the point of it not sealing out water. The movement of the cab will expidite the process, and even worse something happens to cut that boot. Once this happens you will never be able to get at that boot to change it out. There is no room between the cab and the conversion to do this. So most of the conversion mfg'ers have chucked the air on the cab and made a solid connection between the two. As far as ride goes, I have 31,000 lbs on my chassis and it rides like a cadillac. Any bumps in the road are easily handled by the air seats.
2003 28' Show Hauler Motorhome on a 1995 FLD 120 www.showhauler.com