I have already signed a standard buyer agency aggreement.

These are not standardized agency loans.  

Ive called around, and there is Fannie mae agency loans with competitive rates like 5.9%, with a 5/30 amort.

You can use an Attorney, Title Agency, or both depending on the state. 

I just graduated and am currently working as an intern at a government agency (for up to one year).

Depends how professional the current PMC will be about the transistion.First, have client get all leases.Then rent ledgers.Make sure you get a copy of their current management contract, so you understand the Termination requirements - you don't want to break any state agency laws and have the curent PMC file anything against you.Make sure the client follows the Termination requirements BEFORE you take over.Suggest the owner emails their Termination notice to current PMC and copies you on the email.

I personally do both -- I like to have a dual exit strategy on my properties. 

One of the things that make "Agency" guidelines good is that they are standardized across all states so you will not find many differences in Conventional, FHA, VA, or USDA loans. 

The approved contractors have to meet insurance guidelines (often not met by an average company), typically are certified by national and state agencies in home energy efficiency, and invest around $10k in energy testing equipment just to participate.

We do 7-8 flips a year and always use the same local closing attorney.  I'm wondering if it is common to negotiate closing attorney fees due to repeat business for the CA.  When we purchase a property, we have CA fees...