Wow that's a lot to chew through (no pun intended!).
I should probably mention, that I think the main idea of the insane protein, is to counter act the fact I only really have two meals a day. I'm unable to eat after 5pm, I have to take medication daily at 6pm, which needs to be on an empty stomach.
My working hours are 8-5, weekdays and lately weekends. Naturally, this causes me issues with my calorie intake. My main meal is lunchtime, but like most offices our staff facilities are inadequate. We have a microwave, a kettle, and a tiny fridge. Meaning I generally eat out for lunch, which makes calorie counting particularly hard.
I'm 5ft11, currently weighing 9.7st (61.6kg). I started cycling in October 2013, where I weighed slightly over 8st. So I've put some weight on, recently I was hovering around 10st, but I've lost a bit more since increasing the elevation in my rides. I've also extended my daily commute quite considerably.
I went to see this coach/nutritionist as I've been seeing a decrease in performance. I was pretty sure I was overtraining, as I can longer reach anything close to my max heart rate when training. So I sought advice on that topic primarily. The person I saw didn't think it was overtraining, and that I was under fueling myself for the amount of exercise I was doing.
Would be good to get a second opinion, if anyone has any ideas of how I can improve things.
Okay. This is going to be quite a long and involved reply...and it will be a bit of a brain-dump so please accept my apologies for the crappy structure.
I'm making an assumption here that one of your goals is to get back to 10 stone. If you don't care about that and just want to improve your cycling I'd argue that most of this probably still applies.
First of all. For your particular issues this is probably going to be the best source of info:
http://forums.overclockers.co.uk/showthread.php?t=18299646
Basic premises:
Weight loss/gain is a function of kcal in vs kcal out. Obviously more out than in means you will lose weight.
Minimum values for macros are important. Minimum protein intake is important for maintaining muscle mass if you are in the process of losing weight. Minimum protein based on your weight should be between 80 and 100 grams per day. From what I understand of your build (e.g. you have a slight build, little 'muscle bulk', etc) I'd guess that 80 is more likely a good starting point.
Aside from the above, generally speaking protein will help your muscles repair themselves, carbs will help you refuel for (e.g.) cardio-intensive efforts. Fat will keep your joints healthy. That said, all can be used as a source of energy but for cycling (and outside of specific diets, such as keto, which I do not recommend for you just now) you'll want lots of carbs as this is easiest kind of food for your body to turn into "energy".
Meal timing doesn't matter that much in terms of gaining and losing weight. As such your issues with not being able to eat at certain times can be worked around. That said, keeping yourself topped up with energy for your cycling will help you push yourself properly.
Despite what I'm about to say next, nobody can really tell you how many kcal you should eat per day. You can guess at it using various online calculators but if you want to get an accurate idea you need to monitor your intake, your kcal burn and your weight. If you do this even for 4-6 weeks you will have a much more accurate picture than any online calculator or 'gym trainer' can tell you.
Quite note on BCAAs: They're useful if you're riding fasted. If you're not, don't bother with them at all. They work by getting some protein into your blood stream without spiking your insulin. The only time you'd care/bother about this is if you were trying to burn fat by exercising whilst fasted. For yourself I'd recommend instead having a modified protein shake before you set off for your morning ride (see below for more details on that).
General health note: Get lots of green vegetables in each day. If you're struggling with this in your meals then take green beans, sugar snap peas, mange tout or even broccoli with you to work and just snack on them raw during the day. Lots of great nutrients in these and lots of fibre, which is good for your digestive tract and also helps level out your insulin response.
What to do:
The very first thing you should do is to start using MyFitnessPal to accurately log your intake. I appreciate that you're stuck with eating out at lunch but it's perfectly possible to do that and get fairly accurate kcal estimate. Worst case you can grab pre-made sandwiches. Otherwise you can try to stick to (at least initially) meals where it is possible to estimate kcal. If you give us some examples of places you eat at/meals you buy we can help with that.
Hopefully from what I've said above it is now obvious that drinking 150grams of protein in the form of shakes per day is...well, ridiculously pointless. That's not to say that you can't use protein shakes as an effective tool to help you. Instead of drinking 6 crappy shakes per day I would instead have one for breakfast that is made with full fat and/or chocolate milk. For example, use two of
these with one scoop of protein powder and you've got ~600kcal with ~73g of carbs, ~57g of protein and ~13g of fat. You've already ha the same kcal intake as those 6 protein shakes that you were recommended earlier but instead of it all being protein which you don't really need you've got a lot of carbs. I'd actually say that you could just drop the protein powder completely as you'll almost certainly get enough protein in during the rest of your intake.
Assuming that you ride two or three times per day you'll want to time your carbs to support that. Have the above shake as breakfast before you set off for work. If you can't fit in eating until after your lunch ride then at least have a small snack (a small flapjack or some biscuits or something else high in carbs. Don't worry about the sugar content as you're about to do a ride). Finally, make sure you have something substantial between lunch and your evening ride.
I get that you have to take your medication on an empty stomach but do you have any time before bed to eat? If so, get something else in there so you can restock your glycogen levels. Once again, some carbs are primarily what you want.
I'm starting to get a bit tired and don't want to ramble any more so for now I really recommend you work with the above. You need to accurately log what you're consuming as that will educate you more than anything else about what you eat and exactly what macros it provides. Knowing your macros will help you tailor your diet to provide your body with what you need for optimum performance.
On top of the above, something to consider for general health and fitness improvements are strength training and supplements. Of the latter there's not a huge amount of point with most of them but don't discount them completely (creatine and beta alanine have proven benefits, minor as they are).
edit: Oh yeah, estimating kcal burn for exercise is really really tough but I've recently discovered that the Garmin Connect site will give you a very accurate idea of kcals burned on a ride if you use a HRM. It can also feed directly into MyFitnessPal with this data. More details here:
http://www.dcrainmaker.com/2010/11/how-calorie-measurement-works-on-garmin.html
edit2: Regarding your over-training worries - are you getting faster? That would be how I'd measure things rather than HR alone. Then again...what is your training schedule. I can see on Strava that you ride an average of 100 miles a week at the moment. How is that split up?
)! But increasing portion size would balance the increase with more nutrients than just overloading on pure protein like the shake route. Eating more 'protein rich' meals is probably the best way to do it, so things like omelettes, steak, fish and many dairy products are a great source of natural proteins. In fact almost anything 'animal' is good for protein, you're not vegan are you? Cheese is amazing! So is beer! 
