>>Does anyone know what places are good at modifying cars like my mini in California? Also does anyone know what I can do to my car that won't touch my warranty and is not as expensive as the John Cooper Works Tuning Kit?
acisdaman-
Aloha and welcome to MCO,
For California go to the Southern or Northern California regional forums and ask for shops in those areas that will work on MINIs.

To not void your warranty you can do many things. To be really safe you can just drop in an air intake filter- foam like the alta filter, paper like K&N or performance filter like the green filter that turner motorsports sells.
Of you can go with something a bit more obvious like the alta intake with hose- you can check with your dealership service staff to see if they are friendly to aftermarket intakes- if they sell them and do the installs on BMWs then they should be OK.

Exhaust is also an easy upgrade. For the MCS there is the Alta exhaust and the UUC that are grabbing attention.
Many other options exist with prices from roughly $675 to $875.

Lightweight wheelset with non runflat tires are good. The stock wheels are quite heavy.
A rear swaybar that is adjustable is nice and helps handling- if possible use the middle setting or softsetting.

That ought to get you started and please do read the many performance threads. There is much info.