Different school of thoughts on breaking in an engine. On my last build its builder did not want me to beat on it too much and put on some miles before continiuosly beating on it.
But previous to those engines I broke them in beating the living out of it. But those engines did not last too long to see how well the rings sealed with the cyl wall.
You should be able to dyno it and get it straight and baby it for a few thousand miles. Just dont go reving to 7000rpms to find extra HP. I think with the MPX and a mild cam you should it should be out of breath by 5500rpms.
It's not a different school of thought, its all about understanding what is going on during break in and acting accordingly.
During break in the rings are seating (wearing) rapidly. If you use synthetic oil and drive gently it can take over 10,000 miles for this to fully occur which might be longer than a lot of SC folks will even drive their cars in their entire lifetimes. But, breaking the rings in very gently can help attribute to long ring life.
If you break in the motor quickly, you are causing accelerated wear on the rings. The accelerated wear also generates heat. A new engine will make more heat than one that is broken in. Proper operating temperature is important, but excessive heat in the rings and pistons can result in engine damage. It is important not to hammer on the motor too long when it is fresh. There is a difference between a dyno pull that lasts 10 seconds and a WOT run down the freeway that runs 30 seconds as well as there is a big difference in doing one pull vs. doing 8 10 second dyno pulls in a row back to back looking for the last 10hp.
Just how much accelerated wear you want to generate is a function of how long you need the motor to last vs. how much power you need to make and when. For a race engine it is important to have full power as soon as possible. Race engines do not run 50,000 miles between rebuilds so longevity is not a concern.
Another thing that most people don't realize is that a new motor is more susceptible to the damages of detonation and is more likely to detonate than a broken in motor. This is important to consider for those who make a lot of boost on pump gas.
Remember I said that the rings are wearing quickly when an engine is new? Where do you think all the iron filings go? Into your oil. That is why it is necessary to change the oil frequently when the engine is new, and especially if you are going to flog on it when it is new. Remember that when you are "flogging" on it all those metal filings from the rings are circulating in your oil.
Excessive idling and steady load can be bad for a new engine also. Idling will not wash down the cylinders and often the vacuum generated during idle will not really pull oil up into the rings. This means that the rings will load up with abrasives and will not be cleaned or lubricated. This is bad (duh). Steady load will do the same thing only it will tend to over wash the cylinders while not drawing in oil. That is why aggressive normal driving, accelerating and decelerating are the best way to break in a street motor. Highway cruises, big city rush hour traffic, idling, and full throttle abuse are not the best ways to break in a motor if you want it to last awhile and perform well.
In Ricardo's case, I did the initial break in properly (about 25-50 miles) and then I dyno'd the car sufficiently to get a tune on the motor. I asked Ricardo to take it easy on the motor because it was making excessive boost and I was concerned about detonation under sustained load. He informed me afterwards that he ran the car under full throttle at high rpm and sustained load the first time he had the car out (on the way to the Shootout 2007) so I guess if it was going to do something it would have already done it by now. Motors that are broken in aggressively will always make a little more power than those that are broken in gently but at the cost of more wear and shorter over-all life.
You don't have to take my word on any of this, look it up yourself, you'll find many examples and explanations from experts that will all tell just about the same story.
Now as to the effects of a bad tune in a new motor, that is something entirely different. You can completely destroy valve guides and or wash down the cylinder walls and really hurt the motor in 15 minutes from start up if AFR is badly wrong. Any chip can only set up the basic parameters necessary to run before startup. Things like MAF tables, injector values, temperature settings, etc. But if you have something like insufficient fuel pressure, an incorrectly wired injector lead, a bad 02 sensor, etc. then the chip can't possibly do anything about any of that.
It can be very hard to tell on a brand new motor if you have an issue of sorts to deal with. When we start our new carbureted motors on the stand it is always a bit of a nervous session until we get some plug readings and EGT results. Things can go wrong very quickly but once the motor is running smoothly then everything is fine. If you dont' get to the "running smoothly" part quickly then there is LARGE cause for concern. Do NOT drive the car round hoping that it will clear out and fix itself because you will stand a very good chance of doing permanent damage to something in the process.
If you don't have any datalogging capability (as Jason pointed out, you SHOULD have something), then it would be best to run the last known good setup on the new motor. This might mean breaking it in with stock MAF and injectors (!). Yes, contrary to popular belief apparently, you CAN run the stock injectors on any SC motor up to at least about 4000rpm, especially under part throttle conditions. This may give you the chance to verify that mechanically everything is sound and complete initial ring break in and seal without worrying about flooding the motor with 60lb injectors.
I will repeat what Jason said again. If you have a large investment in your motor, it should follow that you spend the money on some datalogging equipment. I have always found it interesting (not pointing any fingers here, just making a statement) that people are willing to pay money to someone to dyno and tune their car (generally $500-800) which will carry no guarantee and is a one time deal that might not even be what you want, but they don't want to spend that same amount of money on tools that will last and can be re-used many many times or even continually if you are the nervous type, that will help them to diagnose their own problems and can be used to verify their tune any time they so choose. For anyone contemplating going to the race track this should be a complete no-brainer.
Technically the motor should run fine with the big injectors, MAF and chip. The parameters are correct in the chip. However, there are unknowns that simply cannot be accounted for with a mail order chip and it will be further complicated by not knowing if there is a mechanical issue (high probability) causing problems. If we had some data from the motor or EEC at this point we'd be a lot closer to solving the questions.