Ok... I'm going to throw in all my experience in this area for wahtever it's worth on. All this was learned the hard way - i am probably the 'Trents friend' referred to above, but not sure.
I bought a set of MPI twins last year from Nathan for my LLY. I was excited just like you are. They got put on at the same time the motor build was happening - so I ended up with ALOT of things to test and troubleshoot after the truck was together and running - and let me tell you we were all over the place trying stuff for several months.
In terms of boost leaks, i had a whole slew of things that went wrong. First i found that each of my intercooler boots were leaking at the intercooler itself. I even bought new boots because the ones i had looked kinda hammered. I was hoping that would solve the problem. Nope. After buttoning those up finally.. i still had a leak coming from down around the drivers side intecooler boot. Turned out to be the intercooler itself - Banks intercooler no less. Banks was quick to get me a new one, but the leak was not something that you could stand back and really hear. Had to have your ear right by it - not like you'd expect a regular leak to be (not as obvious).
So - i figured ok - get the new Intercooler and problem solved. Well - that didn't turn out to be the case either. It did solve the biggest leak problem i had, but here were still 2 others. My original set of turbos had the v-band flange type clamp on the cold pipe tube coming out of the big turbo into the cold pipe. Turns out that the angle was off just a little, and i was losing boost pressure there. Fixed that.
Just when it seemed that we had all the leaks buttoned up, we decided that the turbo i was trying in my small position was just not working out. It was the new Garrett AVNT 3794. Drive pressure was spiking to 100 PSI on a big tune, and still only seeing 40-42 PSI total boost. So we decided to start addressing the exhaust side of the turbos in an effort to find the problem. The Garret turbo came off and i bought a new Danville Stage 2 68mm VNT turbo to swap in its place.
Had a shop in town put that thing on for me - but in the process, somehow one of the cover bolts came out and the gasket started to come out as well. After it was on, for the first time in the 4 months my truck had been running, we heard an audible boost leak. So we went ot checking everything but that turbo. Finally found it. Pulled the cover off, put a new bolt in it, etc etc and got it sealed. Pressure tested and didn't find any leaks.
Drive pressure improved over 20 PSI (seeing high 70's) but still only about 40 PSI total boost. Was starting to get real frustrated at this point. We were getting ready to do a compression test, but i decided i wanted to work on the exhuast side some more... so while the trans was ripped out to put in a new rear main seal, we put on RDL up pipes.
That made a small difference (< 5 PSI drive pressure differnt at WOT with big tune) but also helped EGTs. All these things were goals along with getting the boost # up - so i was happy with the improvement but not happy i still couldn't get enough air... so we continued on testing this and that, checking tunes, checking for tell-tale signs of head gasket problems. etc. etc. Nothing.
Then the big turbo finally let go. You could hear it. It sucked to listen to and to limp it home when it happened. While i was down, Nathan was able to get Max'd outs owner to lend me a spare turbo. It was a smaller turbo (one in the normal MPI kit) - we bolted it on and voila! 48-49 PSI, and even less drive pressure!
Had to run that for a couple months while mine was getting rebuilt. Got mine back, tried it again - even took time to drive mellow for about 150 miles before putting a big tune in - but the first event i went to, saw the same old 40 psi and higher drive pressure - and the turbo came undone again.
Nathan then build me the s480 kit w/ race cover - T6 flange, etc etc. Had that on since just before the WOTE event, and loving it. Regularly see 52 PSI here in Salt Lake, and higher if i go to lower altitude. EGTs are great throughout the whole run... peak at 1600* for a second or two then settle back down to 14-1500* by end of the run. Drive pressure stays below 70 for most of the run, but does start to creep towards 75 about the end of the track.
I know thats a long drawn out story - but it's full of experience that not alot of people were a part of. I had some very smart people involved with the project (and problems) - it took 8 months to get it totally sorted out, 100% for sure - and even then, based on everything that had been tried and found - the opinions were still divided as to what the problem was. I and one or two others were of the opinion it was the turbo itself, which turned out to be the case - but others were thinking that it was head gasket/engine problem, and still others were thinking it was just a flaw in the kit itself - piping and such.
Bottom line now is, i'm glad it's fixed. Thats what matters. I have a rock solid setup that i'm VERY happy with now - thats hungry for more fuel.... i'm just too cheap to provide it.
Along the way, i learned ALOT from much bigger brains than mine - and if we hadn't been so methodical in trying to eliminate and rule things out, who knows how long it would have been to isolate the problem 100%. Symptoms didn't really point to it being the turbo...
Finally - It REALLY helps having all the boost and drive pressure guages. They can tell you in a hurry, IMO, if you have an issue and where. The guage in the cold pipe between the turbos, the total boost guage (prior to intake manifold) and drive pressure (tapped into either side of the truck about as far back in the manifold as you can get it). These tools were very useful in trying to diagnose the problem.
I feel your pain in trying to find the problem, but i'd keep looking for boost leaks. Nathans pressure tester should have a guage on it that you can watch - and depnding on whether you plugged the intake pipe or let the air go into the motor, you should be able to tell whether you have a problem pretty easily. If it's a slow leak into the motor, i wouldn't worry about it. If it drops 5 PSI in 5 seconds - you've got a leak that you may not be able to hear (like my Banks intercooler)... and the funny thing with that banks intercooler - it WOULDN'T leak unless i was pushing at least 40 PSI into the system. go figure....