i gave it a good clean out a couple of months ago, cleaned out all my filters, fans, heat sinks etc.
I built it about 1.5-2 years ago, does thermal compound go off after awhile?
I have one at the front and back and two on the side panel.
I'm guessing the second "CPU load" is a typo and should be GPU load. 90C isn't technically dangerous (max temp is 105C for that model), but it is very high. I have 2x hd5850 and my GPU load temp stays below 75C on both cards.
Are the cards touching, or is there a slot between them? What types for fans do they have?
There is a slight gap yea, They Are just the stock fans for the gainward cards, There are two fans per card.
That's at least part of your problem. That fan style takes air from the front of the fan and exhausts it back into the case. Normally it's not a problem as long as you have proper spacing (1 slot between cards) and case exhaust, but your top card is intaking all of your bottom card's hot exhaust.
That sounds more like your CPU temperature, but I'm guessing your room isn't too hot, right? Probably more around 25C-30C ambient may be more realistic. However, your CPU temps aren't too bad so I wouldn't worry.