<<"Because now I took a 30 min stop over between the train and bus in Zernez; and a 90 min stopover between the bus in Malles and the train. Is that enough do you think?">>
It is routine for Swiss trains and connecting buses to make 4 minute connections. There has been considerable annoyance and grumbling in Switzerland recently, because the trains in and out of major cities are sometimes as much as 6 minutes late during the morning and evening rush hours!
It is a matter of national pride for the Swiss that the trains run on time. The entire system runs smoothly with short connection times because the trains do run on time. On the other hand, late trains are the norm in Italy.
So, for specifics.
A 30 minute connection in Zernez is not necessary, but there is little harm in that. It's been a while since I stayed in Zernez, but I don't think that you'll have to wait on the platform, which might be uncomfortable, because it will be cold in March. There is a small hotel at the station, which has a restauraant, so you will have a place to get a cup of coffee if you have to wait. Since the bus does travel through mountain territory, and the one you catch may come from Malles to Zernez, then turn around, it might be a few minutes late if there is a lot of snow. Just in case, you might check the bus schedule on March 11, using the timetable linked by Chantal. I don't think that there are frequent buses on that route.
Usually in Switzerland, there is train every hour, so I don't worry too much about travel connections inside Switzerland. The place I would worry somewhat ( not seriously, just mild concern) about connections is in Malles Venosta. That train route to/from Merano is very simple, so I'd not expect a late train. We walked from the train downhill to the town, to have lunch while waiting for the bus. I don't recall if we could have taken the bus.
I'd be really surprised if the bus does not take you all the way up the hill to the train station. If, by some chance it does not, I think it is about a 15-20 minute walk. The timetable, combined with the map that I linked will help you on that point.
Google maps does not have enough detail, but you can see a bit about the lay of the land by usin it, as well.
If you turn on "Traffic" under "Points of Interest" in the menus of the "Mapsearch.ch" map, you can turn on icons for the transport stops. Mouse over an icon, and you will get the station name and an abbreviated near-term schedule to/from that station stop.
I don't know the frequency of the trains along the valley to Merano. If I were making the trip, I'd make a note of that information.
<<"And is it wise to book it in advance?">>
I don't know.
In Switzerland, it is never necessary to book on public transport. However, the bus to Malles is somewhat special...it is a Swiss bus, but may have different restrictions. I think I'd try to book the bus, but I don't know how, and I don't remember if we did. I think that it could be possible to book via the SBB ticket shop. You will recall that we booked much of our trip via the SBB, because we came from Zürich through Innsbruck on our way to Bozen and Merano.
The small train in Italy was not full, but, once again, who knows?
If I were making the trip, I'd try to book from Zernez onward, but I'm very cautious when traveling in a country where I don't know the routines. My friends laugh at me for over-planning. ;-)