Yes it appears that the question was whether a 90-day phase-in is included in the 5 years mentioned in FAR 17.104(a) or is separate?
And it appears that it was answered above (i.e., the up to 90 days in the continuity of services clause applies to the incumbent's period of performance, and don't exclude phase-in from successor's period of performance and if that contract/order is one with options then it should not exceed the 5-year limitation in 17.204(e) unless the agency has in place specific procedures to authorize more than 5 years).
A related question is -- shouldn't a contractor be on guard for correctly pricing a government RFP/RFQ that includes both the Extension of Services clause and the Continuity of Services clause?
In those circumstances the government could require the incumbent contractor to perform for up to 6 months and 90 days, respectively, (i.e., 9 months total) beyond the 5 year period of performance, right?
P.S. Seeker - I am new to this board to and I guess can look forward to Copper Members taking cheap shots at my employer/agency if they find my posts painful to read. FWIW, while JJ's post was a bit rambling, it did exhibit his research, rationale, and gratitude for assistance.