First you have to ask is the block rebuildable; is the MMC coating on the aluminum bores in good shape. If not, then you are looking at a new block. I think monkeywrench sells blocks which the bore are coated with NikaSil, which is in many ways superior to the stock MMC coating. Consider replacing the stock pistons with forged pistons compatable with your bore. The "glass engine" reputation of the 2zz-ge comes from two problem areas; the high silicon aluminum stock pistons, and the weak valve train (valve stems/springs/wiped cams). If I was going to go out the trouble to rebuild, I would look at all these areas.
Storm titanium 2005 Elise with carbon fiber spoiler, BWR sway bar, BOE toe links, gPan2, LidBone, sector 111 wheel studs, Grey RAC Monolite wheels with toyo R1R, Team Dynamics 1.4 with Hoosier A6/R6s, Katana2 Supercharger, ECU with 265 flash. PPE headers w/decat, CEL angle eliminator, Silent touch catback, Rear Panel Eliminator, HKS intake, V2 fuel tank, Walbro255 fuel pump. HID lights.