"Plant temperatures are getting far too hot"

edit

I see that you have resolved the plant Loop Temperatures by setting your pump flow to "intermittent".

In regards to the zone temperatures getting up to 40C:

A number non-HVAC factors can increase internal heat gains:

1. Internal loads - lights, electric equipment and heat produced by occupants
2. Solar gains
3. conductive gains or losses - when the outdoor temperature is greater than the indoor temperature, there will be mild heat loads on the building from conductive heat gains. When the outdoor air temperature is less than the indoor temperature, there will be a loss of heat through conduction.
4. infiltration of outdoor air into the space - like #3, infiltration can contribute to heat add, or heat removal. Leaving out

If your indoor air temperature is 40C, I suspect that you may have a lot of glass, and thus high solar gains, and that you are not adequately taking infiltration into account. Keep in mind that occupied buildings in moderate climates do not often reach 40C because the occupants will take action to cool the building through ventilation. If you have taken infiltration into account, you have a lot of glass, and you have a well insulated building, your model may be correct.