Hiya Free,
Sorry I didnt see this post earlier to comment on it. I can certainly understand your feelings on the brakes and battery. I feel the same way. In regards to the R1 Rotors, I have had them on for a few months now and I could not be happier! Even if they are their "E-Line" series of rotors, they are still made quite well! I have NO complaints at all. The stopping power is great and I experience NO fade. Webracin a happy owner of them for almost 3-4 years now without any issue.
Plus as TD said, feedback is your friend. And R1 is right up there with the best and they surly have a HUGE following, 22,000+ feedbacks and almost ALL positive. I would venture to guess to say its a safe bet you will never have any problems with them.
Now to your concerns about cracking. Are there valid concerns about drilled rotors cracking? Perhaps. But with the R1's and several others out there on eBay. They campfer* the drill holes, in other words, bevel them so they are smoothed out to prevent cracking. Will that stop it entirely? Its hard to tell. But I had a set of drilled rotors (noncampfered*) from Tuto Automotive off eBay on my old GT for 3 years and they never cracked. I think its more the luck of the draw than anything when it comes to cracking of the drill holes. If they were that prone to cracking, no one would drill holes in them.
You could always find the "dimpled" and slotted rotors if you are afraid of that issue. But in all honestly I think you will be getting a new car long before you would ever see the rotor drill holes crackings. Just my two cents on that one.
As for the larger brakes. I personally, for now, have just done the 12" caliper bracket upgrade and purchased the 02-05 Monte Carlo/Impala style rotors. You get the "upgraded" 12" front discs plus the standard 10.75" rear discs. I am just using my factory caliper with the 12" bracket without issue. Later on I will get the F-Body upgrade calipers with the dual pistons, but that is something that can wait for now.
Just some things to think about.