Which trains to book now or wait till day I'm there

Book London to Amsterdam in advance. It is cheaper.
Book Amsterdam to Paris in advance with Thalys.
Book TGV in advance. Basel to Gimmelwald wait til you get there. Perhaps you want to buy some kind of Half Fare Card or Swiss Travel Pass if you are staying more than one day.

I'll be in Swizterland for 3 nights/4days still a good deal for half fare card?

Absolutely get a pass for 4 days either Half Fare or Swiss Travel Pass (STP). You have to do more research. I bought a 3 day STP it depends on what you want to see; it is a small country excellent train transport. I road all over the place stayed in Murren. The STP covers most museum s also.

And you should only use the sbb swiss train site not Rio2rome to research travel in Switzerland.

Check your travel insurance will cover all costs before you start booking tickets in case Coronavirus means your trip gets cancelled/ changed.

London to Amsterdam should have been booked months ago for the best prices, although Coronavirus may have led to demand and therefore fares falling. My company has a ban on any international travel from the U.K. and others will have followed, so demand will be down.

you need to buy tickets for all of these ASAP. Prices will only go up if you wait.

For Paris to Mürren (of which Gimmelwald is a part), and Mürren to Munich, you may not be able to do this as a single purchase, because the last leg from Interlaken is a small local company.
1) Buy direct from train operators, not a reseller.
2) Try to buy Paris to Interlaken, and Interlaken to Munich, then buy the last leg separately, either in advance if you can, or at Interlaken station. From Interlaken trains ever 30 minutes to Mürren.

"do I book from Basel to Gimmewald the day of and only worry about pre booking Paris-Basel?" - it makes no sense to buy a ticket at Basel day of, as that involves missing your connection and getting a later train.
"Stechelberg,Schilthornbahn?" is the bottom of the cable car up to Gimmelwald. Rome2rio probably doesn't know the next leg. Look up times on the SBB website: https://www.sbb.ch/en

Munich to Berlin book now

Trains are often even harder to cancel after booking than planes. Given the coronavirus, I would think twice before reserving too far in advance.

You would just pay more for a refundable or flexible train ticket if you buy in advance

This Coronavirus definitely complicates things. I’m not sure if I should spend more and get refundable tickets.

I'm not sure the class of travel affects the refundability of rail tickets. You can buy a second-class ticket that's refundable; it just costs more than the bargain tickets.