1. Loire à vélo is a great route. Paris Nantes is a tad more than 400kms. Take your time and this is a nice week. Should be relatively easy to design a loop. Get a green Michelin guide and have fun.

2. I've carried my bike across France on TGV s (CDG -> Nantes, CDG -> Marseille, lots of other stints) and never had any problem. You can either pre-book specific trains and my understanding is that there will be a designated wagon where you can roll your bike (as is frequently done on TER (regional). OR you remove the front wheel, pedals and turn your handlebars sideways, put your bike in a bag (Rinko or padded flight bag) and it'll be treated as a regular piece of luggage that you carry yourself on board. You will not be able to store it inside the luggage compartment of a standard wagon, but can leave it near the entrance. Just go to your bike when the train stops so that you can move it around if needed. (Not easy to explain, but obvious and easy in practice)

3. Disbelief reading the warning about Calais. The encampment called the jungle has been cleared years ago. Apparently rehabilitated into a nature reserve. I don't recall any incident involving refugees back then.