No vacuum leaks, no EGR problems, too lean probably means ignition is good. A 6.5 power valve is a "late opener" - doesn't open until engine vacuum falls below 6.5 hg. That's basically when you floor it, for the first few seconds you have WOT (as in passing cars on the highway). One other way to enrich your mixture is to get an "earlier opening" power valve - I think a 10.5 is the "earliest" Holly sells. Holley advertises the rule of hg/inch at idle divided by two, rounded down to the nearest .5 size. So for my jeep, idle vacuum is 23 divided by 2 is 11.5 - the power valve Holley would recommend is the 10.5 which would open up alot. I'm more in the economy mode - I'd rather save ga$ by cruising with just the jets - so I keep in the 5.5 power valve which opens up only on the highway for passing basically. By the way - the Checker Auto here in Gilbert has a huge selection of power valves, jets etc for that carb. (you can buy them online also).
I'd think your 48 jets should be fine - if you are at Yuma you're almost at sea level. Here in Gilbert (1200 feet), I actually ran 44 jets for awhile, but the engine is alot happier (and runs cooler) with the 47's. 44's were good for the mountains.
However, I found this post on another site: I am at sea level here in Virginia, the jet we ended up running were 55's. I tried a set of 47 than 49 and it just didn't run well. It would idle but no power and poor performance was easily noticed.
Take it for what it's worth.
I highly doubt it's your accel pump since it's new and you can see it work. That basically just gets you out of the hole shot anyway. Sounds like you are lean well into midrange rpms. If you've got no air leaks, my best guess would be too small jets and/or a too late opening power valve.
All this advice may be worth exactly what you paid for it!!
is a pretty good source for MC2100 information.