On the speech and debate clause claim:
Just as a search warrant does not trigger the Fifth Amendment's testimonial privilege, neither does a search trigger the Speech or Debate Clause's testimonial privilege.....
The purpose of the Speech or Debate Clause is rather to protect the independence and integrity of the legislature by not questioning Members of Congress for their legitimate legislative acts.
....Just as the Fifth Amendment does not protect a person from disclosure of incriminating evidence, the Speech or Debate Clause does not prohibit disclosure of legislative material. Rather, it prohibits a Member from having to answer questions as to his legislative activity. Here, Congressman Jefferson has not been questioned about actions that fall within the sphere of legitimate legislative activity.
On the separation of powers claim:
The statement by amicus that if the search here is upheld, in the future the Government need "only to persuade a federal judge" to obtain warrants to search other congressional offices, is a gross trivialization of the role of the judiciary. Amicus Brief 33.9 A federal judge is not a mere rubber stamp in the warrant process, but rather an independent and neutral official sworn to uphold and defend the Constitution.
If there is any threat to the separation of powers here, it is not from the execution of a search warrant by one co-equal branch of government upon another, after the independent approval of the third separate, and co-equal branch.
....Finally, the Court finds no support for the proposition that a Member of Congress must be given advance notice of a search, with an opportunity to screen out and remove materials the Member believes to be privileged.
....Rather, the principle of the separation of powers is threatened by the position that the Legislative Branch enjoys the unilateral and unreviewable power to invoke an absolute privilege, thus making it immune from the ordinary criminal process of a validly issued search warrant. This theory would allow Members of Congress to frustrate investigations into non-legislative criminal activities for which the Speech or Debate Clause clearly provides no protection from prosecution. "Our speech or debate privilege was designed to preserve legislative independence, not supremacy." Brewster, 408 U.S. at 508. The execution of the search warrant upon Congressman Jefferson's congressional office did not violate the separation of powers principle.
On the 4th amendment claim, that Jefferson's lawyer wasn't allowed to be present:
The Court finds that there is no right to have one's counsel present during the execution of a search warrant, that there is no exhaustion requirement to the issuance of a search warrant, and further that the affidavit contained no false premise. The search was reasonable under the Fourth Amendment....The Court is not aware of any authority, and Congressman Jefferson points to none, that holds that the right to counsel extends to the execution of a search warrant.
Update: Analysis by TL commenter Scribe:
My short take on the opinion is that the judge is not about to wall the Capitol off from warrants. It seems he's relying on lots of older (60s and 70s vintage) precedent on the scope and protections of Amendment 4, but while he gives that with one hand, he takes with the other. I didn't bother to count how many times he talked about the warrant being reasonable, etc. Lots of orotundity about no man above the law and similar, but that's just sugar with the castor oil.
Short advice to any congresscritters - make sure everything your office does and has in its computers is in some pretty-direct way definitively related to legislative activities - be it legislation, proposed legislation, hearings, etc., because if you don't then (especially in light of Hudson v. Michigan) this case says your mahogany doors ain't gonna stop the FBI from coming in and taking it, and the judges will back the cops.
Big win for the executive, even though the judge intones "trust us, we're neutral judges" way too many times.
