I haven't done alot of welding in recent years, but do some on occasion. I have been involved with some sizable projects over the years, and I learned to weld @ about 10 years of age on a farm...(if you broke it, you better learn how to fix it).
One method which helps prevent warping is to tack-weld on each side of your lap joints prior to making a hot pass (similar to the stitch weld already mentioned). Using staggered positions of the tacks on each side first, and then, match all tack welds for the opposing side. This will partially bond the work pieces so that movement can be minimized before the heavier welds are applied to the metal. Tubing and right angles can warp from the high heat of welding as well, so keep this in mind when building smoker frames, legs, etc. Clamping the pieces (when Possible) can help, but is not a 100% cure for the problem.
One thing to remember is that when you apply a weld to one side of a piece, the weld bead can pull as it cools and shrinks. If you have a tack weld on the opposite side of the weld first, you can counter-act the shrinkage/pulling from the hot pass weld. This doesn't guarantee the metal will not warp, but can reduce it's effect/severity. Also, as your welding progresses, take a few moments to eyeball or measure, fit check, etc...this is especially important when fit is a high priority. By doing this, you will know if things are going to get out of control before correcting it will become a major issue. If things start to look out of wack, then, a good smack with a hammer will break the tack welds loose so you can get things back into shape...just remember what happened and if you need to do something different to prevent it. Think of it as low & slow cooking...take your time and watch the results of your efforts...give yourself time to react to unwanted conditions, so you can more easily take positive action.
If you just can't find an effective method to remove the warpage, you may need to grind out quite a bit (or most) of the welds with an angle disc grinder, reshape it to the form you need, assure proper fit, and then start with the tack weld method.
Believe me, I know what you're going through...it doesn't exactly put a smile on your face when you discover it, and it's not fun to fix at all. What ever happens, be patient and in time you will be rewarded for your efforts.
Best of luck!
Eric