I removed my CPU fan and heat-shield to give them a clean as they were caked in dust. When I built back up again, the system turned itself off during boot-up. I removed the case to make sure all connections were OK. I rebooted the PC with case off and it worked for 10 minutes then switched off again. I left it turned off for an hour, then booted up and checked bios menu. I noticed that the CPU temperature was running at 89 degrees centigrade for a theo temp of 65. All fans in unit are working okay and at correct speeds. 
Ouch! A computer that hot is good for cooking eggs, but not for running properly. A CPU temperature of 89 degrees is one in need of some quick cooling. I’m guessing that you were having problems with heat already and that is what prompted you to clean it out in the first place. Taking the cover off and cleaning it out with canned air is a good first step toward troubleshooting your problem, but in your case, it may not be enough.
Troubleshooting Cooling Issues
I want to make sure that you have adequate airflow around your unit. Is it sitting on a soft surface like a carpet or bedding? Make sure that it is either on a hard surface or elevated just a little off the floor. Make sure the vents aren’t blocked by anything and that air can intake and exhaust from the unit.
Heatsinks
You say at the end of your question that all “fans” are running - how many are you using? You may need more than one to cool the PC, depending on the demands you are putting on it. Are you using heatsinks as well? This may be what you are referring to when you talk about a heat shield. An active heatsink is a device that attaches to the processor and attracts and dissipates heat from the unit into the air with a fan. A passive heatsink does not have a fan attached to it. Any kind of heatsink device needs to have some sort of thermal compound on it that creates a seal between the heatsink that the thing that it is cooling. Some new heatsinks come with a rubber thermal compound pad already attached and some require that you use a thin layer of paste. If you remove the heatsink, you need to put more thermal compound on it, even if it came with a pad. Apply only a thin layer - too much or none at all will compromise the ability of the heatsink to work properly.
You’re going to have to try a few different things - fans, airflow issues and heat dissipating devices in order to cool your PC down to a safe temperature.
