^I'm not going to change intake other than porting it and port matching it for optimal flow. I'm just curious what the cost is for the valve job for the future maybe.
Also I know the 550 is not hard on it's cam chain but I want a flat sided cam chain because it will be that much gentler on the expensive NOS cam chain tensioner I'm putting in it and i figure it will require less maintenance and stretch less being a cam chain thats 20 years newer. I'm aware that "old school" chains of all varieties can be stronger than their lighter modern counterparts. You're saying the NOS honda chain stretches less than the DID cam chain? I thought the Honda chain was made by DID?
As far as jetting I'm mostly concerned about clip position because at some point in the future I'm going to do 4 into 1 exhaust with a muffler and pod filters.
Here's a question; what assembly grease should I use? for the stud threads etc? The "Genuine Honda Moly Assembly Paste"?
here's another question; are HD engine studs worth it?
Honda's OEM chains were made by RK of Japan, mostly. DID is not a top-quality chain, more of a 'consumer grade' sort of chain, inexpensive but usually effective with adequate maintenance. It the realm of 'riveted-together' masterlink cam chains, in my experience, these are the ones where the link let go, most often. Back in the days of the Twins with the masterlink'd cam chains (CB160/72/77 bikes), many of those were DID, with a clipped-on type master link.
Use the HD engine studs if you're going big-bore, or if installing high-dome type pistons with compression higher than about 10:1. Otherwise they are not really needed.
The jetting: the pipes do not affect this need much, the piston bore even less. If you realize that the larger bore causes the airflow thru the carb to be slightly higher at a given RPM than it was before, you'll soon realize this implies there will be no significant change in flow over the jets in the venturi: this results in the same mixture. This is a long-way-around to say, "No, bore change does not imply carb rejetting changes". Higher compression might, if going past 10:1 CR, to reduce ping: usually simply using higher octane does this better, and fouls fewer plugs in the process.