it's called 'sequential' printing.

I would say that those items are probably not suited for for it in your printer.

Bear in mind the height of the finished item, when the printer finished one, it must reset the printbed for the next.
The height of the first model will either prevent this, or the model will get caught by the printhead.

Haven't used the latest makerbot software, but due to the design on the machine - it's not well suited to sequential printing, so it's quite possible they haven't bothered implementing it.

But as has been said - your extruder should not clog. Printing 4 things at once should not be an issue, as long as your temps and extraction settings are good - should do that without any real issue.

I've done 26 items at the same time on my dirt cheap i3. And often do multiple items simultaneously on my replicator clones.
The only machine I've ever done sequential printing on is my delta, which can easily avoid the print nhead hiiting previous prints. But even there I'll usually do simultaneous prints - just easier.
And you actually WANT each layer to 'dry' (actually cool) before the next is laid down. Gives cleaner smoother prints. It's the reason for the print area cooling ducts.

So don't think that's your problem.

Can you give more details of exactly what's happening ?