I wasn't clear. That is exactly what I meant. It can certainly be done and it has been. If by some miracle (or by the vigilant work of a very good machinist) the flange on the header and The flange on the intake are the same thickness (+/- .001") the system will not leak if provided with equal clamping pressure. The original equipment intake/exhaust manifold also must be flat and the "ears" (the relief into which a washer sits where the studs and bolts pass into the head) should be checked with a micrometer to ensure they are the same thickness. But that happened once in a factory in Toyohashi, Japan so it is likely to be much closer to spec.
Also, there is no real performance benefit realized from a header on the 2F. Some might disagree, and there is the benefit of knowing you will not crack your intake manifold with hot exhaust gasses. But freezing the flapper in the diverted position or installing a block off plate between the two halves of the OEM I/E manifold ensures this also.
Short version: if I were in your shoes I would put the intake from the old F engine on the new 2F engine eventaully. Check it with a straight edge to be sure it is flat. Do the same with the head, get an oem toyota gasket, and torque it together. Unless you have an engine stand it would be safest and easiest to do that after you install it in the truck anyway.
It may be tempting to leave it as is because it is all together and ran just fine. I wouldn't blame you if you did. Come to think of it, just run it with the header for a while. If it works well...great. But dont get rid of the old engine and it's I/E manifold, carb, and down pipe. You may want them. They do swap directly.
