Couple issues after motobox install

I finally broke down and bought a motobox, I installed it this morning before work and I've noticed a couple little issues...

When driving down the road and I pull in the clutch, the RPMs only drop to around 2k for about a second before it drops back down to normal... It used to drop instantly to idle. The 2nd issue is when I blip the throttle more than about 1/8th turn it stalls (It almost sounds like it chokes it out).
I've been running this map for about 3 months: '08 akra map with klinks pc111 map.hex (so Akra slip, Motobox, Hooligan SBV)' without any issues at all, I left that map on and did the 15 minute reset when I finished the install. I also installed the MH secondary flies.

I double checked everything and couldn't find anything I left unhooked, I also checked with TuneECU and didn't find any codes... Anybody have any other ideas

You possibly knocked the TPS sensor while you're doing the install.
You can readjust it by feel (needs the watchmakers touch!), with a volt meter or of you have tuneecu.
I got up really early this morning so for the heck of it I can't remember the voltage it needs to read with closed throttle so you have to do a search here.
It has been discussed as people tried to adjust it. It needs to be done with engine warmed up otherwise the "choke" keeps it open.
You'll know when it is right as it straight away starts to run fine with no hesitation or high idle.

Another thing could be that you didn't pushed the inlets all the way in to the rubbers. Check also for bend or jammed linkages.

Does the throttle feels free btw?

My bike is always 'slow' in dropping revs after I've done a 15 min reset. It sorts itself out after a couple of short rides.
It has never stalled though...

Thanks for the replies...

The throttle feels great, it only has issues dropping to idle under load, if I give it some revs in neutral and chop the throttle it drops straight down...but if i'm riding and chop the throttle/pull in the clutch it has the issues.

Try putting the stock secondary 'flies back in and see if that helps. At least then the only change from when you know it last ran properly (other than the possibility of having accidentally knocked something out of adjustment) is the MH box.

If that doesn't cure it, try the MH 'flies with the stock box and go from there.

Failing that, set the whole thing back to stock and start again changing one thing at a time.