I think you are asking the wrong question(s)

>> Since hotels have a 3pm check in i know we would need to book the night before and let the hotel know.
I don't know that. I would ask the hotel what the options are. Early check-in, day rate, or worst case is chill in the lobby for several hours. You could have the hotel hold your luggage until check-in time and go out for lunch, visit a nearby site. I would wager that they will have a room available before 3PM.

>> 35k marriot certificates(which i don't think we can use in tokyo) a couple hyatt certificate, a couple hilton free night certificate.

You sh/could be asking how best to use those certificates. Staying at the 60,000-yen+ Tokyo Hilton for free is a no-brainer to me. Status benefits like free breakfast make it an easier choice. Same for the Hyatt Regency which happens to be across the street from the Tokyo Hilton. Split your stay between the two.

Along with the certificate nights, use the Delta and Cap1 credits to pay at least part of the cost of additional nights, or for the cash part of a cash+points night. Or pay additional nights with points.

You can use Marriott points in Tokyo. Can't you use a 35K certificate as 35,000 points toward a stay? I see two Tokyo properties that were 37,000 points (May 14). Can't you use 1 certificate plus 2000 points for a night?

If you book and later pay with certificates and points then you don't care about exchange rates.

Today, your $200 can get a room that costs 30,000 yen. Come May that 30,000 yen could cost you $230