The system is all connected, please go through all the settings and check why only 2 or 3 meters are reading.

I think it is unrealistic with one etherpad to attempt to read all the meters every half an hour, because of the bottleneck. It could conceivably work, if every meter have little to say. Please set them on daily until you get all to communicate and up to date, and then you can move some of them to every half an hour where important?

Please see Tools->ProblemMeterList, and View->MeterReadLogs for complete reasons why not read. In most cases it seems it is because of the bottleneck. To fix this, please change your Automatic Read Interval in Edit->Advanced Settings to daily. (you can use Tools->BulkEdit to change them all at once - tip: use FireFox if you use bulk edit)

Can we force only one meter to read

Yes. Easiest is to go to Tools->CommunicationMonitor for the particular meter, and if it is busy, click on Abort Current Session. Then click the checkbox of the set you want (e.g. profile); and Start Read.

When it downloads the readings, is it only current or is there a history

There should be a history (profile)

Why are some meters shown in green and then the next day yellow

A yellow meter means that it has communicated successfully in the past, but the last reading attempt failed.

How long should it take to do the download

It depends on how much history it is downloading. Elsters can sometimes take a very long time. If it takes more than 2 hours to download 2 months, something else is wrong. It should take less.