thanks for the reply Hush. after fiddling with it, i am almost 100% certain nothing was put together wrong, as the only time anything concerning the front axle was disassembled was at a bike shop my buddy works at, and he is quite meticulous when it comes to disassembly and reassembly. now, from what i understand the caliper is a floating caliper, and i opened it all the way up with a c-clamp on the piston when fitting it back on the bike to have ample room to get it on with pads installed. there is absolutely no fluid in the system, as we had some work to do with the master cylinder and caliper, mostly cleaning, but the old fluid wasn't pretty anyway. we haven't had a chance to fill it yet, but if i'm correct in that it's a floating caliper, would the fact it's completely opened and has no fluid in it have any effect, and possibly make the caliper poke out closer to the wheel than it normally would, when at a filled and actuated resting position?
as for the clearance issue between the tire and fender, i've concluded that my fender got tweaked somewhere along the lines of things getting shifted around a couple dozen times in the garage. the gaps are perfect in front of the mounting brackets, they're only a bit off behind them.