Sine sweeps are one of the best test signals you can use to capture impulses. You can generate sweeps inside the Deconvolver itself.
In theory it is possible to remove a reverb from an acoustical recording given the room's impulse response at the recording position is known. In practice this may not work well, because a real sound source (if it's not a speaker cabinet) is hardly ever in a static position while deconvolution requires that the performer stays "still like a rock" relative to the microphone and room's borders. These small movements of the performer usually result in various "swishing" artifacts making output of the deconvolution process unusable. On the other hand, the farther away the performer from the mic and reflective surfaces is, the lesser the chance the aforementioned problem will manifest itself.
Various "hardware" impulses technically work like reverbs, but they "color" the sound instead of adding reverb tail - hence, they should be used at 100% wet level. Note that compressors cannot be modeled with usual WAV impulse files - only their coloration is applied, not the compression itself.
Yes, this is normal: this means your recorded signal had a lot of leading silence. You are safe to remove this leading silence.
Deconvolver's test tone generator wasn't designed that way - the sweep runs from minimal to maximal frequency to cover the specified period of time. So, only the first and last frequencies cross zero strictly.
You should probably insert some amount of leading and trailing silence when running the sweep through FX, so that the recorded file stays several seconds longer than the sweep itself.
This problem is known: the fact you get a trace of the original sine sweep in the deconvolved impulse file tells that the device (in its particular mode of operation) you are recording has some sort of non-linear behavior - it may have harmonic distortion or chorus/phaser like behavior happening. This situation cannot be resolved by any means, because Deconvolver can only produce impulse responses of linear time-invariant (LTI) devices (rooms).
Unfortunately, the minimum-phase transform is quite an unstable technique, so the sonic problems you are hearing are to be expected. In general, there is no much sense in using the MP transform since it mostly is an experimental technique. In practice, when you record, for example, a speaker cabinet, it already has a minimum-phase impulse response, so there is no need to additionally force it to be minimum-phase.
It is not necessary to normalize the files before you pass it to Deconvolver.