The OP can apply for the study visa after he arrives in Germany. He has to got to the Ausländeramt (Aliens' Office) in Germany to get his residency permit.
I think check-in should not be a problem since the check-in agent will see the following in his/her system.
21AUG13 / 1426 UTC
National USA (US) /Embarkation USA (US)
Transit Netherlands (NL) /Destination Germany (DE)
ALSO CHECK DESTINATION INFORMATION BELOW
Netherlands (NL)
VISA NOT REQUIRED.
Netherlands (NL)
Vaccinations not required.
Germany (DE)
Passport required.
- Passports and/or passport replacing documents must be valid
for at least 3 months beyond the period of intended stay.
VISA NOT REQUIRED.
Minors:
- Minors aged up to/incl. 15 years of age may be included in
the passport of a parent or guardian, provided
For details, click here
Additional Information:
- Valid visas in full or expired travel documents are accepted
provided For details, click here
- Visitors are required to hold proof of sufficient funds to
cover their stay and documents required for their next
destination.
- This country is a Schengen Member State For details, click here
Warning:
- Passports must be signed by the bearer. Passports without
signatures will be accepted if: For details, click here
- Passports and passport replacing documents issued more than
10 years prior to date of travel are not accepted.
Germany (DE)
Vaccinations not required.
CHECK TINEWS/N1 - EGYPT
Timaticweb Version 1.3
21 August 2013
The border control in AMS will not be a problem.