Others have offered good advice so far. Big tires, even tires that are simply bigger than recommended but will fit on the rims, reduce the handling capability of your bike. They're a bad idea, unless you want to go slow around the corners. I'm not a fan of the whole "brat" thing, and "brat café" is another amalgamation that someone simply made up. When people build "brat" seats, they frequently just put a flat seat pan on the frame rails (usually after chopping off the support between them). On the CB550, this support sticks up a little, so when you put a flat seat on it the rear tire rubs on the underside of the seat as the shocks compress (exacerbated by those big tires). This is very dangerous. And of course you lose the stiffness that the support provided for the rear end of the bike. The advice you've received about clip-ons is correct too -- ergonomically, you're going to need rear sets. Running the smallest possible tail light also reduces your visibility to drivers behind you, something to think about.
These changes aren't just a matter of aesthetics, they are a matter of function (and safety). Ultimately, it's your bike, but seabarney's advice is spot on -- run a stock bike for a while so you know what it feels like, then make some decisions. If you do all the things you're proposing, you may be permanently altering your bike in a way that you'll regret when you realize just how badly it performs. Again, it's your bike, do what you want, but while some people may think bikes like that 750 look cool, anyone who knows anything about bikes realizes what a shame it is to do that to such a cool bike.
Once you get a 3k mile tune up done, run your bike for a while. Your compression might come up a little. Although some of your numbers aren't even and on the low side, I think your bike will run ok, at least until it gets worse (unless it gets better!).