I too am always looking for ways to minimize my "kit" for longer trail runs, especially mountain runs where its easier to give in to bringing along unnecessary items "just in case". Not sure anyone can touch Krupicka on the subject of minimalist travel in the mountains, save maybe Joe Grant. Weight adds up quick and when you're used to running with nothing but a pair of shorts, shirt, shoes and some water for miles, it all can feel heavy adding stuff (shell, gloves, headlamp, calories) when you're trying to move quickly and light unimpeded.
As far as carrying nourishment, I manage to stuff 4 gels per handheld pocket, that's good for a 20+ mile run if I don't guzzle all my water and I conserve, if I need extra I can stuff two gels extra in my shorts pocket but that's about it otherwise they flop around or pull on my shorts. Sometimes I'll wear a small Nathan waistbelt/fanny pack on long runs that stores extra gels, calories, salt tabs, pair of gloves, its non obtrusive and minimal (2-3oz.) and most importantly doesn't bounce or rub weird, I find it a better solution than loading up my split shorts with Gu and calories which always tend to bounce and get weighed down with sweat after a while, that's distracting. The ties on shorts don't do a thing really. A gel flask is another minimal option, they fit in your palm and eliminate the need to stop or bite open wrappers.
Those little 8oz. handhelds are good for short runs, that's about it, good enough to wet the lips. Have you considered squeezing a gel or two into one of your small handhelds and nipping on it occasionally throughout your run? This eliminates the need to store gels or spent wrappers and keeps you fueled enough for short stuff.
As far as sewing pockets onto shorts, make sure you keep them low profile, maybe even consider a material that has four way stretch so items don't bounce around. As close to the waistband as possible as well. Raceready is a brand that makes some shorts with lots of pocket storage, they're pretty solid, but items bounce a bit IMO.... plus the shorts are pretty hideous but eh, you'll be sweaty anyways.
For the longer stuff, a hydration vest is pretty nice, especially when you're going self supported or minimally supported ( spread out aid stations), but those vests always seem to feel cumbersome after a bit.
Ultimate direction has a small clip bottle, as does Fuel Belt, u might consider those. If you only need 4-6oz. then just fill your mouth up and breathe through your nose, sip as needed. ;-)