For the HH...there is a setting for HH opening>more closed, or more open I think. And make sure your TD3 HH pedal is calibrated. And then you need to set up Trigger cancel (I can't remember what its called) in the TD3 brain....Did you reset your Brain first....you should even if new. Then near the end of the manual there are all the midi and trigger settings....flip through that to adjust the setting that makes the most sense.
In the midi mapping section on the lower right hand of the GUI there is a dopdown for all the different hit for the particular drum you've selected (via right click).
So for example if you pick the snare it will show you midi note assigned for the type of hit in the dropdown. If you change the selection in the dropdown to rim...it will show the note assigned to rim.
Go through this process for all the drums, and all dropdowns deleted every note assigned(can't remember of right click>delete, or if there is a "remove mapping selection).
Then go back to the first drum you want to set up Eg: snare, select the hit you want to map....you can also audition the with the large audition button before mapping......select learn and hit your TD3 snare.....pick next dropdown...lets say rim, then select learn and do a rimshot (as in the manual of the TD3).
Use this process to complete your mapping....then save your midi configuration...(i can't remember how to do that either....you'll figure it out)
Also, de-select samples for the drums you are not using to limit sample size loaded into RAM....your good to go.
You can now pick any kit, and load up your midi setting (I told you to save) and you can use any kit with your TD3
HTH
Cheers!