I guess you don't have the stock pipes anymore. There is a bumper stop on the stock exhaust to keep the Center stand away from the chain. You'll have to fabricate some kind of replacement stop to take its place.
I'm not sure I understand the brake lever complaint. A hard lever is usually desired, as all the lever pressure translates into brake disc pressure and indicates a sytem totally bled of air. But, perhaps you over tightened the pivot bolt for the lever? Does it return to at rest position easily?
Or, perhaps the brake pads and disk are contaminated with brake fluid, grease, fork oil, or silicone lube? A reduction of friction down there would mean higher handle pressures to get effective braking friction.
If the pads were ever contaminated, surface cleaning is ineffective. They are porous and when they get hot the contamination oozes out again and acts as a lube. Replace with new pads and take care not to contaminate them. Oh, and thoroughly clean your brake disk, too. Clean with a solvent that doesn't leave a residue and dry completely.