Here's a few things to try. Is the firmware up to date? Did you do an SMC reset? With regard to the PRAM, I vaguely remember that to do a full reset you have to hold it for 3 chimes. What format did you put on the SSD? How is the spinning disk connected?
Dear jakobk, I have the same issue, but slightly different. I started with a 2013 system. for reasons that are explained here I changed the CPU for the 4790. Mine too won't boot up. So I have a new CPU and a new mother board and it still won't boot. I'm interested in your progress, what you eventually did and if you confirmed the lack of compatibility with the CPU.
OK, I did it! I popped out the system board and removed the heat-sink and as expected, big gobs of grey paste. I cleaned up both the CPU, GPU and heat-sink with IPA (alcohol not the beer) then applied the Arctic Silver. There isn't a specific guide for the Mini Server Mid 2011, but this one was pretty close and I used it to guide me. The only differences I found were the position of some of the screws. Things I learned (1) Removing the wired connectors, you must pull UP not in the direction of the wires or the gold contacts pull out! (2) The power connector is pretty stiff but comes off with little or no issue (3) The T8 sprung screws holding the heat-sink down have pretty shallow heads, so make sure your screwdriver is in good condition and the tip is not mullered (4) I don't have a 'special' tool for removing the board. I tried with 2x screwdrivers, as I had read, that didn't work for me. I found that some gentle pressure on the front edge of the board pressing against the round opening was enough to get...
I'm also tempted to clean and reapply the thermal paste. I got my mac mini server on Saturday and was shocked at the 'tickover' temp and the 'load' temp. I too was seeing temps over 90C but the exhaust cooling air did not feel that hot which immediatily made me think of the themal paste. I redid the paste on my 17" MBP CD (Not C2D) and cleared out the heatsink from fluffy stuff. That helped! When I was turning the mini over and over working out how it all fitted together I realised that the intake for the air was only around the rim of the removeable base, it can only have been around 1 or 2mm wide, makes me wonder if that isn't a restriction to the flow. Would be interested in others thoughts.