Tim's Stage 3 Skyline .049s start out as stock SureStarts. From what I can tell, he lightens the piston, resets the piston/rod clearance, polishes the cylinder, checks for proper piston/cylinder fit, ultrasonically cleans everything, and modifies the shape of the venturi. He also includes a custom head which uses Turbo glow plugs. The crankcase is machined a bit on the outside for appearance and anodized in the color of your choice as well as a custom machined spinner. He also includes a custom machined prop driver and adapter which allows the use of APC props of different sizes by simply turning the adapter around to fit(nice touch). There may be more to it, but those seem to be the noticeable differences. The prices range from $40 for Stage 1 to $60 for Stage 3. I haven't run mine yet, so I can't tell you about power and performance gains over stock. Raindave has one and may be able to compare it to a stocker. One thing's for sure, they are beautiful little engines and the uniqueness of it was enough to make me buy one.
If you've kept up with the Hypercolor/Tim Wiltse saga, you already know that he's been AWOL for some time now. His website is still up but I understand that he hasn't been shipping orders lately. I received my engine in September just before he quit responding to emails.
http://www.hypercolor.biz/index.html