A little more data is needed to accurately identify the discrepancies.
1. Does the truck really weigh 5000lbs? Has it been weighed? Don't rely on somebody's word or some published numbers. Get it weighed at a track or a truck stop.
2. Where did the 400hp estimate come from? Most automatic drivelines lose about 20-25%. This equates to about 300-325hp at the wheels if it really makes 400hp.
3. What kind of dyno is it? Is it a Dynojet or a Mustang Dyno?
4. Yes, 2nd gear is not good for measuring HP. You could easily lose another 10% or so this way.
5. In second gear it is possible for the tires to spin on the dyno. Not likely, but possible. Look at the graph, does it have any strange dips in it?
6. You say it runs "high 13's". Be more specific. What is the best it has run? Mph is more important than ET.
Having said all of that, the comment about dyno's skewing numbers on purpose is most likely directed at a shop which uses a Dynojet. The Dynojet uses a standard load of *I believe* 2000lbs for all vehicles. This allows heavier vehicles to accelerate much faster than they would in real life, thereby skewing the numbers a certain percentage. The Mustang dyno allows the operator to specify the load placed against the vehicle. This lowers the readings (usually about 20% I think). It raises the question also of just how much load did the operator put into the machine for the testing if it is one of these types of dyno's.
One thing you need to remember about dyno testing is that it should ALWAYS be used for comparison purposes only. The actual numbers are not to be totally relied on. A dyno should only be used for evaluating the effectiveness of parts and for tuning (well, and bragging if you get good numbers.
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That being said, if it really weighs 5000lbs and runs high 13's, then the HP calculator that I believe IS real world accurate puts the motor at somewhere near 340rwhp which would put it over 400hp at the motor. But this is only as accurate as the #'s you gave us which I think you really need to verify before you put much stock in these numbers either.
Bottom line, I think the dyno guy is out to lunch.