I'd just use tape myself. The plastic on zip ties is quite hard and can make knocking sounds if it vibrates against the wood. If you use them, use them in places where the wires can't move much, or else use them in conjunction with a self-adhesive pad the tie goes through.
The tone pots in the kit have a liner taper. This is one reason why the tone roll-off is all towards the bottom end of travel. Some people like that, I don't so I fit audio taper pots on volume and tone. Volume pots should really be audio taper (though if you always play with lots of distortion you may prefer linear pots as the sound will clean up quicker if you turn the volume down). Tone pots are a personal choice. I now always use 250k audio pots for tone regardless of whether fitted to single coils or or humbuckers as you do get things happening a lot quicker. Still not a lot between 10 and 8, but you can definitely get a lot more going on below 8, though there's still normally a final sudden tone roll-off below 2. But that's too muddy a tone for me anyway, so if I do use the tone control, it's all in a wide and controllable portion of the pot travel.
Using 250k pots on tone for humbuckers does knock a very tiny bit of the treble off compared to 500k pots, but it's a very small amount indeed to my ears anyway). I tend to pick fairly bright sounding humbuckers, so it's not an issue for me.
The tone pot is a variable resistor, which simply limits the amount of output signal flowing through the tone capacitor. The tone capacitor makes a low-pass filter in conjunction with the pickup coil's impedance (not the tone pot resistance). So a 500k pot will stop more signal flowing through the capacitor than a 250k pot at full resistance. But the actual difference in the guitar output tone between 500k and 250k resistance is really very small indeed, and I really can't hear it.
But if you note that 250k pot on '10' is the tone on '5' setting for a 500k linear taper pot, you should see why using a 250k pot gives you far more controllable range (basically the useable range is doubled). An audio pot further shifts the tone action further up the pot's travel compared to a linear pot, so the tone on a liner pot set around 3, should be the tone with an audio pot set on 5.
All this is personal preference. There is no right or wrong way, but 250k and log/audio taper pots work for me on tone.
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