Rpm's stop increasing when accelerating

I purchased my 2007 Subaru Legacy around a year and a half ago, and
had to have a new transmission and head gaskets replaced. The car was
ran with bad head gaskets for several thousand miles, forcing me to
replace many external engine components as well, due to damage from
the oil. The old transmission was replaced due to extremely hard shifting
from second to third gear. 15,000 after all of the repairs, my car is running
great for now, and getting serviced regularly by myself including oil
changes, new air filters, etc. The new confidence I have acquired due to
my car running so well, I am able to "carve the roads" as one would say.
Since I am no longer afraid to drive my car how i want, high RPM's are
visited frequently. The car runs amazing, and shifts well in the manual
mode of the 4EAT. although it runs and shifts smoothly, there is one minor
issue.
    When accelerating from a stop, i usually allow my car to reach 5000-
5500 RPM's before i shift to the next gear. when doing this i notice
something very strange, which has confused my college automotive
professor, and even my mechanic. First gear follows through with
accelerating perfectly, having a even increase in speed and RPM's. Second
and third on the other hand, are quite odd. When in second gear my car
reaches an area between 3900 and 4200 rpm's where the car RPM's will
stick and stop accelerating for around 1 second, and then it continues on
accelerating to the shifting range into third gear. In third gear, when my car
reaches an area around 3400-3700 the car drops about 300 rpms, before
continuing to accelerate normally. All this happens with my foot pressing
the pedal about 75% down, and doesnt happen all of the time. This occurs
about every other acceleration, especially when going up a hill. The engine
light has not appeared, so we have no way of knowing how to fix this
problem. Does anyone have any suggestions?