Have you seen anyone about your knee? Its getting close to the event, but a physio/sports therapist may be able to relieve the pain enough to let you participate. Most people will pick up aches and strains during training, and its sometimes useful to get someone else to assess how serious they are.
As cougie said, very few (if any) people would ask for the charity contribution back if you don't take part. No one would want you to get seriously injured during the event, so people understand that you have to pull out of events.
An alternative would be to use the Shoefitr online application to see how it compares to your existing shoe.
If you go to the runningwarehouse.com web site and find the guide 7, then click on the "show me how it fits" option. This will show you how it compares to your existing shoe (NB as its a US site, the sizing is american rather than UK).
You can't buy from here as they are US only, but you can then translate this into the correct UK size for you. I found it useful when I got a pair of very cheap Saucony Fastwitch (coincidentally from Wiggle!) as the shoefitr advised to go up half a size from my current shoe, which was also a Saucony.
As 198bpm is the highest, I'd use that. You could round that up to 200 bpm as I suspect you could have (theoretically) gone a bit higher unless it was during an all-out sprint at the end, or whilst climbing a steep hill on the course.
As you've said these weren't abnormal spikes in the trace, they all sound genuine readings.
I'll be the first to mention Pfitzinger & Douglas and their book "Advanced Marathoning" that will provide an excellent explanation of what you need to do to run a faster marathon, and also includes sample 18 & 12 week plans.
Even if you decide to use alternative plans, the explanation of the various training sessions etc will help you understand the 'whats' and 'whys' of marathon training.
Personally,I prefer to follow a plan for a target event as otherwise I find I either skip runs or get into a rut of "I'll just go for an easy run of xx miles today". Whereas, when its written on paper that today is '9 miles with 5x 1000m' I feel obligated to do it.
As the 18 week plan is roughly four months, this would start for you in Jan/Feb next year for you. Prior to the plan, your training focus will depend on how you ran the 3:51 marathon. If you ran it 'comfortably' with a fairly even pace throughout then you want to focus on improving your speed and maybe train for a half-marathon for the next few months. If you struggled in the latter stages of the marathon, you need to look at your endurance and get some long,steady runs (e.g. HADD training) in before starting the plan.