TTT: Relax! Comrades is still six months away. You say you "Can't afford more time off due to injuries" but if you don't rest now it will take you longer to get back to fitness properly. You were cycling even when you weren't running much the previous two weeks, so you won't have lost much fitness. You'll be able to return to your previous levels quickly - so long as you allow your body time to repair properly now.
I hate to say it, but you may have to take a longer period away from running to really let the tendons settle down. I tore my left posterior tibial tendon in a cycling accident and ended up in an Aircast PTT brace for five months (it has an air cushion under the arch, so the posterior tibial doesn't need to do any work). I then returned to running VERY carefully. I wear half-length off-the-shelf orthotics (in my minimalist shoes) most of the time to reduce strain on the tendon (it has a scar, so will never be as strong as if it had never been injured) but I also run barefoot for strengthening.
Main exercises were with resistance bands, progressing to single-leg heel rises. Also proprioception exercises. I was headed back to ultras, and had run as far as 26-27 miles, when I broke my ankle five months ago. Now I'm heading back there again (longest run this side of the break being 16 miles, so far).
Real food not junk food. Enough protein for muscle repair and growth. Enough energy intake to fuel runs and repairs. Enough vitamins and minerals - preferably by eating a varied diet (lots of different vegetables and fruits) rather than taking supplements. Enough fats for essential fatty acids and fat-soluble vitamins. After that, it's what you find effective. Experiment.
For during the runs... Whatever works for you. I like fig rolls, malt loaf, Kendal mint cake (which is just sugar, glucose and peppermint oil), jelly beans, green-ear Percy Pigs (I'm vegetarian), cheese sandwiches...
Now thinking of running the SVN Dymchurch marathon, end of January, to make sure I've covered the distance and am basically qualified in case something goes horribly wrong and I have to skip London. I suppose with several 50-milers under my belt in the past (as well as a few shorter ultras and a couple of marathons) I have the advantage that i know I'll be able to cover the distance by then - I have 10 more weeks to play with - but I'm not going to be fast, and I probably ought not to push it at London, five weeks before Comrades, so I guess I'll have to accept I'll be in one of the back pens and just going for a finish for Comrades this year.
Five months since I broke my ankle. I ran 16 miles this morning, in a time that I won't bother sharing! From Coulsdon Town, up Farthing Downs and following the London Loop back to our clubhouse in Croydon, then back home to Beckenham with a little diversion to make it 16 miles rather than just over 15. Feeling quite pleased to have managed that - it's only five weeks since I ran six miles for the first time since the fracture.