They may just have needed the time to work on what they found on Dynkowski's computers, and to trace all the IM messages, bank accounts, brokerage accounts, and so on.
I doubt the feds needed two years to do that. The raid was just to get probable cause from a grand jury to tap everything and anything to expose the entire organization.
The feds probably have every PM,IM, phone call, Matt and others made in the last two years.
2 years of investigation before an arrest is probably RICO.
Thats why the indictment says.
"Along with others known and unknown to the grand jury to commit an offence against the united states."
The grand jury does not even know how deep this goes.