Ok, start by reading
THIS thread.
1) By reading that, and a couple other posts, people are flat-lining HP just above 5000 rpms. This is because of a couple reasons, partly because manifold is horribly restrictive, and flows less than a stock PI plastic intake. The second was that the blower was crap. As you can see, people just can't make power with the series 1. The 2000 S-281 was rated at 350 hp @ 5000 rpms. Yes, only 5000 rpms.
2) The MAIN question you have, yes, dyno's can be different. Mine was tuned on a Mustang dyno to 669/621. A year later on a dynojet it was 718/626. Same car, just different dyno types. In your case, I don't know how much it is off. He says 12-14% off, then it may be a Mustang dyno. So, 321 +12% is pretty close to 360. I don't think you are getting any more than that.
3) The blower itself sucks! I don't know how else to say it nicely. Saleen bought the G3 M90 cheap from Eaton. They had a lot of them because they used them on several GM models in the 90's and the Thunderbird SC.....all v6's. When those programs ended, Eaton had blowers to spare....that's where the 99 (and some 98) supercharged Saleens came from. When Eaton started running low on the G3 M90's in 2000, Saleen moved to the G4 M90. Much better design, a ton better in the VE department. Minor changer to the intake manifold increased power only by 15 hp, but moved the redline to 5800 rpms. It wasn't until 2003, when Saleen did it right by moving to the Series IV, and Lysholm twin screws.
If you get 400+ rwhp from a stock blocked 4.6 with a series 1 SC, you might be the first. I think about the max I have seen with similar mods is ~360rwhp. Even then, the blower gets so hot that driving it much will cause it to pull timing due to the excessive intake heat.
Lastly - A graph is needed to see what is what.