Reducing the DB on the wireless should help, experiment by reducing the DB, have a listen and look and make sure you are happy.
also worth checking out the Kemper input tutorial:
Kemper Profiler Tutorial - Input Section - english
Hope that helps.
1) would be akin to rolling off the volume knob on the guitar a smidge.
Personally, I'd go with option 2 to not having to be dependent on the wireless unit.
For Clean sens: adjust to avoid red light
For dist sense: Here I would think like for a "real amp": hotter output on a guitar naturally drives a real amp harder anyway. I leave my dist sens at zero for this reason. Other people might like to use it to adjust rigs across the board to have the same amount of overdrive from their chosen profiles regardless of whether they play a strat or a beast with active pickups, so to speak. Both are valid approaches.
Keep in mind that you can make an "input preset" for each guitar (which includes among other things the clean and dist senses).
I would probably setup the Kemper input first without your wireless system, then adjust your wireless output after accordingly.
The distortion sense is used if you feel the guitar is breaking up too soon (lower it) and not enough (raise it). Clean sense is to balance the clean level and distorted level so you don't get a huge volume difference between them.
If you have other guitars that already have sounds you like with your wireless and KPA, options 1 or 2 may be counterproductive.
3) You can adjust you new pickups to sound the way you want them to sound without making any changes to your wireless or KPA.
No, clipping the input (as in "digitally", re. the LED lighting red) is done with the CLEAN SENS. Apart from this, to get the desired amount of amp distortion/compression, you adjust the dist sens. The two are not related - the dist sens is simply a "global" adjustment of all profiles' gain value.
People usually lock the input section (with its settings of the two "senses") so they don't change from rig to rig. Be aware that locking the input section has to be done separately for browse mode and performance mode.
Just play with clean sense, i.e. lower it. Although if your wireless signal is too hot when you play through any device, I'd suggest you lower the db as you suggested.
Bottom line is, don't sacrifice on tone. You may have to try reducing a bit of both to get an optimal sound.
Also make sure where you are clipping/distorting. When I set the level for a guitar I make sure to shut off all effects, as they can add unwanted volume to a rig ( they can be a cause of unwanted distortion).
Wow thanks for the quick feedback this really helps!! If I change the clean sens will I need to increase the volume output for the clean profiles? Sorry for all of the questions.
No 
Look in the manuals (there's a link in my signature)- There's also a FAQ that might mention something about clean sens and dist sense, can't remember what's included.
