1. No idea, unfortunately- I have no experience with that sound card. It has to have a control panel entry of some sort where you can configure the clocking.
To get to that control panel, open up SX. You then go to the Devices/Device Setup/VST Multitrack tab, select ASIO Driver, and in that window you'll have entries for driver selection, clock source, and a button for "control panel". First, make sure the right drivers are selected for your card: click in the driver item and look at the entries in the popup. There should be something like "Delta 44 ASIO" in the list. Make sure that that is selected.
The clock source item should then be automatically set to "settings". Push the "control panel" button, and that should bring up the Delta driver control window. Set the clock source to "internal" or "master", whichever appears in the panel, and set the other audio settings like sample rate to whatever you want- check the Delta documentation for their recommendations. That ought to do it.
2. The recording will drop out automatically whenever the cursor passes the right marker, if the auto-punch-out mode is turned on. To check this, pull up the Transport panel. it will have an entry for L, for R, and four buttons below it: AQ (auto quantize), auto punch in, cycle mode, auto-punch-out. Make sure that auto-punch-in and auto-punch-out are not selected (white instead of blue). You can then click the mouse in the R marker field and set it to any value you want.
I use templates to do this sort of needed-every-time setup. I get the program into the most commonly used setup (channel assigns, track names, input and output state, auto-punch-in and -out turned off, and the right marker moved out where it won't piss me off). I then do "save as template", and save the template to some name I like, like "basic setup". Then, when you start a new project, you choose "basic template", and all the gozintas, comesoutas, and so on are already set up the way you want them. _Big_ win.
3. No clue. I know nothing about Halion, because I don't use it. When I do MIDI sequencing, I just play directly into Cubase, edit it there, and let it play back out. I don't do that much with MIDI- just very basic stuff. I've never seen anything like this.
Fragmentation on the drive has nothing to do with this. I defrag regularly, but drive fragmentation really only becomes an issue when you have lots of audio tracks in a project, especially at high bitrates. I'd certainly defrag the beast, but that isn't the problem.
Anybody else want to take a swing at this one?
Hope that helps...