Let's see if we can make this a bit simpler for you.......commence long ass post....
Buffers are usually necessary when running a long chain of effects/cabling due to signal degradation through the long length of cable that the signal has to travel down. Your chain does not appear to me to be that big (this is coming from someone who runs 18 pedals at all time, with 3 buffered pedals, a Whammy 4, a Boss Giga Delay, and a Morley Little Gator volume pedal). Signal degradation usually occurs in the form of losing high frequency (and very rarely, low frequencies, with shitty buffered pedals from the 70s and 80s). A buffer evens out this signal loss by effecting the signal impedance. While a boost does not do the same thing, a boost would in effect help to strengthen the signal and retain high end loss as most boost tend to add a little high end. While I've never had any problems with buffers before my fuzzes (and I have 7 on my board), I also run a mild amount of compression first which will (1) slightly boost your output signal (2) give a little shimmer to the top end. I also run a boost after my fuzz chain and before the volume, whammy and delay. Why? I just love my boost, it's always on and it does add the perfect amount of top end clarity.
The Crybaby Q's buffer sucks. I've had that wah, and while it's a great effect, the buffer does suck (tone). I've not heard any noticeable degradation through the whammy or most boss effects; their buffer is good. The real question is in a detail you have left out: what amp are you playing into and does treble and high end make up a good portion of your preferred tone?? Again, I don't notice a significant difference between plugging into my chain and plugging in directly into my amp. But I also play a Marshall (treble bite for days) and a vintaged pup'ed Jazzmaster (also will bite your head off with the tone up all the way up). So a little bit of high end loss probably helps me at the end of the day. I feel as if those who are most worried about signal degradation are those who use humbuckers, which have a naturally darker tone. They need all the high end they can use to keep their cleans from sounding like mud. I remember when using an old 80s ibanez delay and flanger with my LP (with modern, high output humbuckers), the pedals would fuck everything up. Using the same pedals with my tele or jazzmaster, didn't bother me: I roll a little and a moderate amount of tone off anyway (respectively) when using those guitars.
So in the end, there's no quick and dirty rule. If you are experiencing tone loss because of your wah and whammy, TB loop those suckers out of your chain. And, no, I don't even understand why you would think putting a shoegazer after your loop and a high quality od before your loop would be a problem. Most people put whammy's and pitch shifters first in chain, to get the cleanest, unaffected signal. I don't, but that's because I love when I run a high gain fuzz into the whammy and turn it on; it becomes like a digital wash. Further, if the wah doesn't effect the sound of your shoegazer being before it in-chain, more power to you. But I personally like wah after fuzz, because I'm a noisy motha fukka.
Bottom line: if you like how it sounds, do it. No one here is gonna tell you the "proper" way of setting up your effects chain, though it's good to know how these things interact with each other. But there is ALWAYS exceptions to any "rule."
