OK, so Dynojet don't have a default map for the Jardine Slip-on you have - I'm in the same boat with a Viper race can...no problem.
While not ideal, you can experiment with any of the standard maps Dynojet provide on their website (or software CD that would have come with your PC3
The best place to start is with M110-001 which is the basic map for a completely standard 954 (you are talking about your 954 right ? - its just you don't mention which bike you trying to sort...). Go for a ride and see how it feels, ask youself when riding, does it accelerate cleanly without bogging or flat spots ?, does it hold constant revs at a steady light throttle (like when you're riding through town at 50KpH), is the exhaust note even on hard deceleration or does it pop and bang ?...then go from there by noting what issues you have, and using the map compare software to find another map that addresses the problem you have identified...
I took my time, did some research on the Net looking for slip-on design info, and rode my bike over the same route trying different maps until I was happy with what I was using (I settled on the map for the Akraprovic slip-on).
The other way which will deliver a better result is to pay to have a custom map made for you by a tuning shop with a dyno...
As for the flapper mod - I haven't done it because I still have my Htev in place and figure Baba san knew what he was doing when he designed them in the first place...if I had a full system then I'd do the flapper mod too.