Your fine either way, the fuel map will work great, mainly the extra fueling is helping down low where the stock map is way lean.I probably should have phrased that better. What I was asking is if it would be a problem running a map for a bike with the secondaries removed on a bike without them removed.
I did a couple of short commutes to and from work and everything seemed ok. Right now the bike is in the shop getting a new TPS & the TBS sync done...and I'm in Michigan for work until Friday night. Saturday I'll have a chance to take a long ride and see what's what.
Pulling the secondaries will increase the throttle response down low and make the bike snappy feeling so I've read. Thats not really desirable to me, the bike doesn't need any more throttle response IMO. They also effect the 5th and 6th gear performance, but its my understanding they mainly increase intake velocity at lower rpms and smooth out throttle response. They obviously were designed to serve a useful purpose. Many threads on the subject, most say it makes teh throttle response "crude". Probably fun to do if your a pavement only pounder and like an abrupt throttle. Probably feels like my old 07 FJR before I put the aftermarket throttle tube on.