More than likely it is a failing graphics card, they tend to be the weakest link of all the components in Mac Pros.
Check all connections for the card and that it is seated correctly in the PCIe slot.
Easiest way to confirm it is the graphics card is to take it out and put in another one.
Do you have access to another graphics card, or can borrow the graphics card from another similar Mac Pro.
Replacing the graphics card is a simple procedure there are many You Tube videos, make sure you select
one for the 2009 Mac Pro.
The graphics card you replace it with will depend on what you use the mac for, there is no point buying a
high end card if you only use the mac for e-mail, web browsing and low end apps.
If you use the mac for 4k video editing, 3D modelling or other high graphics intensity work then you
will need a graphics card that can handle it, this will run into hundreds of dollars/ pounds etc.
To retain the start up screens and access to the Startup Manager/ Boot Manager then the card must
be a Mac Edition or 'flashed for mac' card.
Standard PC cards can be used in a Mac Pro but you will not get the boot screens or access to the Boot Manager.
While you are agonising over the decision of which card to buy you can get the cheap Nvidia GT 120,
this was the standard card that came with the 2009 Mac Pro. This is a low end card but will get you up
and running and are always available, they are second hand though and will cost about $60-00.
Make sure it is the Apple card, the one with the light grey cover.
It has one DVI and one mini Displayport outputs so depending on your monitor you may need to
buy an adaptor.