Usually when I do that sort of campaign, I keep spawn chance to 0% for the first two jumps from each point in Sol, or something roughly like that, and then turtle hard for a while. That way you're only dealing with precursors and swarm (unless you had an NPR at start, get really unlucky, and your starting NPR is right next door). If you want to be absolutely sure, don't start with an NPR, spend a long time in a relatively small number of systems teching up, and don't turn the spawn chance up until you've got sufficient tech/numbers to hold them off for a while.
You're basically never going to win against a 1000% difficulty NPR from a standard start unless you get supremely lucky in how much buildup time you get -- against a freshly spawned one, you'll probably want at least TL5-6 and dozens of capital ships, and against a spawn-at-start one at least an effective 1-3TLs above them and scores of capital ships built specifically to thin large numbers from range, as well as a long chain of systems you can fortify with PDC missile bases, minefields, monitor-type JP campers, &c.
That, or a ship with excellent cloaking device, thermal sensor, thermal output reduction on the drive, and a planetkiller bomb. Alternatively a bunch of fighters with the last. Pull an Ender's Game if you find their homeworld and plaster it with meganukes instead of trying to kill their fleet, then whittle it down while they slowly repair their industrial base.