One thing you may notice on the E4OD after service is an
increase in the whining noise it makes especially right
after startup.  This is normal for the earlier vintage pump
used.  The later pumps are much quieter but, not worth the
effort in an otherwise good trans.  For some reason, they
quiet down in most cases after a couple thousand miles.
There are a couple of additives like LubeGard red that can
reduce this whine and improve the shift characteristics of
the trans.  This and one other are the only additives I have
ever used in a transmission and found to have any benefit as
far as doing exactly what they are advertised to do.  Many
of the shops in this area put it in every rebuild job
caliming it greatly reduces the number of performance
problems.

The gunk you saw in the pan is also quite normal.  It is a
collection of the wear material from the trans clutches.
The clutches wear just like the brake pads or the clutch in
a manual trans vehicle.  It just collects in the fluid to be
carried to the pan where it is "stored" until you service
the trans.  Service interval for the E4OD is in the 25-30K
mile range which should be fine unless you are known to have
overheated it at some time such as when towing more than you
should have or stuck it in the mud and abused it.  The
clicking you heard is also a normal part of the E4OD but,
was probably louder than normal as the solenoid pack is
normally submersed in fluid when the trans is "FULL".  It
was probably louder because it was not full at the time.

You should now be experiencing some level of personal gain
from having done this yourself.  It wasn't too tough a job
and you can use the $100 you save to take the wife out for
the evening and make her happy with your other handy work.

Cheers
Lugnut