You may indeed need to start over. AI progress of 1000+ is pretty substantial, and one of the things about AI War is that pretty much everyone simply loses games once in a while. It's all part of learning how the game works.
It's tough for me to say exactly what went wrong since I didn't see the game unfold, but I'll do a little math. 1000 AIP/20 progress minimum per planet=50 planets taken. This isn't counting things like special forces guard posts, warheads, or on the other side of things data processors or similar things. That seems pretty close to what you've got on the map.
I think that a lot of those conquests could have been avoided by better scouting. It helps to remember that in most cases, taking planets helps the AI build things rather than hindering it. So for your expansions to be a net gain for you, they should be directed towards things absolutely required or at least extremely helpful, such as advanced research, an advanced factory, core shields and so on. It's not that hard to skip territory with transports, especially early on.
That having been said, you might be able to survive this cross-planet attack with the right tools. CPAs tend to bunch up outside your wormhole before going in, so a lightning warhead or two might help reduce their numbers a bit. Since you have a huge amount of territory, you might be able to rebuild some of your fleet as they charge towards your home world, especially if you can slow them down enough with turrets and such. Good luck, let us know how it went.