Some important points regarding diagnostic approach:
When patients with chronic disease (such as Wegener's) present with an acute problem, one should consider if this is a process related or unrelated to their underlying disease. Attempts to evaluate the "activity" of the chronic disease should also be made.
When patients are admitted to hospital, careful thought should be given to what tests are ordered at time of admission. Although we should all try to attempt to minimize unnecessary investigations, if a patient is going to be in hospital for more than a few days it may be helpful to get "baseline" CXR, ECG and "routine bloodwork". This will may serve as a useful comparison should they develop further complications associated with their admission diagnosis or adverse events from hospitalization or treatment.
A 1997 NEJM review of small vessel vasculitis is available here.
A review of the evidence of PCP prophylaxis in non HIV infected patients is available here.