Stock headers won't seal

[Lil bastard]

They are likely leaking from heat warpage. This can happen even to factory collectors, especially if they're not properly torqued.

As mentioned, the solution is to have them decked. But, removing material from the flange will only increase their propensity to warp in the future.

To minimize this, ensure you're removing as little material as absolutely necessary.

Set up a dial gauge and take as many data points as you can, especially from around the ports and only machine the flange as deep as the largest variation. You can use a straight edge and feeler gauge too, but it won't be quite as accurate and you may remove more material than necessary.