Firstly, the rubber boots. They are just there to protect the piston, so there isn't an immediate problem. You should, however, replace them as soon as possible - if water gets in it can, eventually rust the piston into the bore.
I'm not sure if a repair kit is available. The 145 manual covers the replacement of the boot & piston seal, which implies that a kit is available; the 156 will use a similar, if not the same, caliper.
The soft pedal's a bit of a mystery. I assume you haven't disturbed the hydraulics, i.e. you've just screwed the piston back into the caliper to fit the new pads. It may be that the new pads just need bedding in; several stops, starting off gently & gradually increasing in severity should take care of that.
It shouldn't be necessary to set anything after fitting new pads - that should happen automatically, but that assumes everything was correctly set before you fitted the new parts. The handbrake cable will be adjustable - on the 145 it's at the lever end, accessible by opening the gaiter round the lever.
Hope this helps.....now, if anybody can help me with Honda CBR600 front brakes........