As we have seen, even R3s with full exhaust systems can benefit from increased air filter flow than the RU-2780s provide. With a modified engine, you will benefit from even more flow.
I am a Carpenter Racing dealer and have seen their quality of work on Hayabusas and GSXR1000 engines before they started with the R3. If they did not offer quality kits, parts, and work, I wouldn't deal with them.
I have a few customers with Carpenter kits on sportbikes used for grudge drag racing. These engines are regularly run hard and put away wet, season after season. Some are running as much as 150 hp of nitrous with pusher systems on top of the bored/stroked engines, and are still running strong.
If you are going to do the Carpenter package, do the pipe as well . With the intake cam having different intake valve closing points than stock, this will dictate different intake and exhaust lengths and diameters than stock cams - as will more compression and higher VE (volumetric efficiency). Your Jardine header and exhaust system is limited in what it will do on a modified engine.
The stock rods are very nicely built - they have regularly turned 8800+ rpm without issue. And we are working on getting improved aftermarket rod bolts. You could even consider shotpeening and balancing the rotating assembly for more safety and smoothness.
The R3 block is STRONG. Lots of webbing and support.
The Carpenter kits use very good quality pistons, rings, and pins. The valve springs and Ti retainers are able to last a long time. Their cams are re-grinds using a smaller base circle, ground and treated by a very good company, so no issue there.
So the only issue is increased wear from running higher rpm occassionally. At stock rpm points the torque is actually improved substantially, so you can putt around town, and still have more output than you do now at common engine speeds and loads. Then let it lose on the open roads, or stoplight to stoplight and watch the sportbike riders expressions.
Feed it good oil and filters at regular intervals, and the engine should last a long time.
Talk to Art and Bob at Carpenter Racing. They can answer your questions in detail. Just do so earlier in the week if you want to spend time on the phone with them - early in the day is best. They are busy this time of year.