Received wisdom on cables for me has always been to use as short a run as possible to maximise quality. Also, the type of cable will make a difference. I used to use planet waves cables, and got background noise that I never really thought about... then I replaced them with Van Damme cables and get zero background noise. The cables are about 4 times more expensive though.
On pickups... all my guitars have DiMarzio, and most are Ibanez. The PAF Fred Pickups in the bridges of my JS guitars are awesome, and I've fitted this pickup to other guitars with great success. Evolutions are also amazing... go to a store and play a JEM or JS to get an idea of the sound. Both guitars are basswood, so in the same family as yours, and you should get a good idea of the sound.
On amps - a good small tube amp would be a Cornford Harlequin... I have one - 6w and amazing tone, but they are boutique and expensive. A cheaper option could be the lower wattage Laney amps. I also use a THD Hotplate on my Laney TT, which brings it down to an acceptable level for use in the house...
Hope that helps... :)
Oh, and I think most people would like to punch Bono... there is a southpark episode which deals with this topic brilliantly... PM me for details ;)
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