I think that you should be able to run Armageddon 2089 with the 3.5 handbook. There will be slight differences in the skills and skill names, Sleight of hand/PickPocket for example (I cant rememebr off the top of my head which of those is 3.5 and which is 3). but since most of the edition specific stuff in the PHB is in the sections you don't need for A:2089.
Having said all that I've never played A:2089 yet, though I recently bought the core rulebook for it.
The main difference is likely to be any changes to the skills and feats from the PHB used in Armageddon, check the lists in the Armageddon SKills and Feats chapter. I don't know how many of these has changed between 3 and 3.5
That probably wasn't that much help but hopefully it'll give you a few pointers.
If there's anything else i can fail to help you with :lol: just post and I or someone else will be glad to help I'm sure.
LBH