You're going to get lots of different suggestions I expect but I'll start:

Brakes: I've got a set of these:

http://www.bikebandit.com/bikemaster-brake-pads-shoes?m=147605#tabtop

Quiet, bike stops fine. They are organic,not ceramic so they may not last as long as pads made of harder material. I haven't had them on long enough to comment on that. I think ceramic or semi metallic pads are more likely to squeal though.

Tires: Shinko 712 front and rear.

+1 on the EBC organic brake pads.  On my bike they were a big improvement over the stock brake pads.

There have been many good tire threads.  You put on a fair amount of miles so you would likely benefit from one of the better brands of tires like Metzler, Pirelli, and others.

If youre putting 50 miles a day on it 5 days a week PLUS goofin off, havin fun AND running it,, what? Year round? 10 months?
1,075 miles/ month, just goin to work,,add your estimated RF&G miles
( RF&G = Running,farting & giggling)/month,,multiply by months /year you can ride like that.
The way Im lookin at it is, youre laying down enough miles to justify as classy a hunk of rubber as is available. Id look for the tire that gives the most miles, period. Ive run Dunlops that were reasonably priced, but only gave about 5,000 miles, but I didnt try to stretch them, I was playing, hard. Well, as hard as I dared, Im really sorry, but I just cant think of the names of the higher class, highway type tires. I know they cost more, but if you can get 8,000 miles or maybe 10, & NOT be payin someone to put a new tire on & not be down while its being done? Hey,, theres $30.00, at least around here.. Id pay $100.00 more for a tire that went twice as far. It would actually work out to be savings over time,.

Ya know, I really cant remember just what I got on the Dunlops. I Think I went thru 2 of them, on the rear & I THINK I got 5 to 7,000 on them,.,I am sure I wasnt exactly excited by how long they lasted,, Nothing was ever as slick as that stock rear,,That thing felt scary in turns.

Hmmm... strange

if that's your choice, I'd go with the
ME888 100/90-19 & ME880 140/90-15
although I'd prefer the 888 on the rear and the 880 on the front for probably even life.

or go with the pirelli's

The taller aspect ratio on the rear corrects for a slightly off speedo.

the rear tire should give you 16 to 20k miles
not sure of the front, they usually give 2x life.

P.S. In Ontario, Canada, we have an HST, a harmonized sales tax combining both provincial and federal taxes on almost everything we buy that runs a whopping 13 percent.

11" on center or taller shocks.

Although my 98 has the exact same 140/90-15 Cheng Shin on it now as a full modified that it wore as a stone stock platform. Seriously, the exact same 20K+ miles so far, less than $80 tire that was installed in 2000 or in 2001. And the thing still has 50% tread or more left...  

Some Savages they fit in with no problems, others they do not. Depends on the tire brand more than anything else. And run it at 40psi, it will be narrower than at the stock squishy recommendation.