No, I think the curvature of the seat stays remained the same, but the chain stays are different - the 99 are slab-sided at the front, whereas the 98 are round. I expect that makes the 99 stays stiffer, although I hope it doesn't mean you have lost too much vertical compliance, as I've always found my E4 very comfortable - certainly relative to the harshness I'd read about in aluminium frames. I don't think the down tubes differ, and I'm not sure they could as there was only one Easton Elite down tube available. Your photo does seem to confirm that the 99 frame doesn't have a mount for an E-fit front mech. If fattiman posts some shots of his frame, we'll see that they changed the chainstay design again for 2000. So quite a few detail design changes there, maybe the chainstays being the most significant, but they must have thought it was still the same basic design. Or maybe they just liked the E4 name for some reason, and didn't want to change it?
T90112120 is another new one. It seems they had the frames made at various factories over the years. Mine is an F (Fairly works), some are A (A-Pro, the main Orange builder), most 99s seem to be MT (I don't know the builder) and I've even seen one quoted as G (again builder unknown to me). For 200 frames a year, that's quite a lot of builders! I haven't heard the explanation for that, but they must all be good builders, as Easton would only allow Elite to be used by selected builders in those days. I've always assumed that the 200 per annum thing is true. Otherwise, why say it? The frames were priced at £550 BITD.