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She was who I was seeing after TCR. I'm not sure she thought Transiberica was a good idea at the time but it was her that made it clear if it was getting worse I should bail and so I took that into the event (along with a 42T cassette!)
Building up slowly makes sense but you have a fixed timeline so sometimes you have to choose an option that isn't the best in terms of recovery, to hit the longer term goal. Then again, I'm a fucking meathead and nothing I do is likely healthy so maybe just stick with your original plan :D
You can do longer events in place of shorter events. They might even be good training if you're aiming for PBP. I don't see the point of qualifying with the bare minimum if you can do more and still be fit for the main event.
Depends on the nature of "knee niggle". I've ridden across the US with a knee niggle so they're not all super serious. I'd probably see a physio and look at what might have caused it, lower my gearing and then ride the planned events anyway - with a bail out plan in mind if the pain is too bad. That's what I did for Transiberica after fucking my knee up in TCR.
Going in to an event with an "I'm allowed to bail if this issue gets worse" mindset takes a lot of stress off.