I finally had some time to expiriment with those ballasts. I got 2 pairs of endcaps and 2 different T5 bulbs. I tried a 24" first to see if it would even fire. All looked good. To my surprise, the 24" T5 produced a brighter light than a single 96w PC. The bulb seemed hotter than normal though.
The next bulb was a single 36" T5HO. Again, it fired right away and was super bright. It was definatly better than the one of the PC bulbs and possibly as bright as two. After doing some rewiring, I decided to try 2 x 39W T5HO. Again, both fired and the light was brilliant. The bulbs were still a little hotter than I thought they should be.
The 24" bulb surprised me the most. It seemed brighter with this setup than it did in the old T5 setup I am currently using. There was only one way to confirm this. I pulled my old retro setup out of my tank and checked the bulb with my old ballast. It was noticably dimmer. The bulb was just as hot as it was in the new setup when I was done, so I didnt worry about how warm the bulbs were anymore. I guess that was normal.
I let the ballast run for a while to heat up. The ballast never got too hot to touch. The enclosure that it is in also has a fan on the end and airvents along the top. I dont see heat becoming a problem.
As far as I'm concerned, the "engineer" that I emailed about this is an idiot. He told me that it wouldnt work at all. I sent him a picture of the "Dual 96W PC Ballast" firing 4 x 36w T5HO bulbs.... no reply.
Now I have new lights and all I have to worry about is burning down the house.