Hello:
I am doing a 5 lugs conversion with 3.5 inch 911 struts. Going to get 5 lug rear arm with parking brake conversion. What type of brake set up would you guys recommond (both front and rear) . Boxster or 968/944 turbo? Which one has bigger brake pad area?

Thanks

It really depends on what your requirements are. Larger pad area is not the only consideration when deciding on a brake combination. What HP is your engine going to put out. Bigger brakes require more HP to get up to speed.
Boxster calipers seem to be a better deal. They are newer and probably easier to find, restore and fit to the struts. They do require an adapter to mount, however the 951 will require both machining and an adapter. There are several variations of each model caliper, and the brake rotor must be matched to the particular version of caliper. You have to engineer a solution, not just slap on whatever is handy; especially when it comes to having front to rear balance.