Just to answer some of your questions.
1) I don't know about the JamPoints. I was absentminded and ended up with separate accounts for my iOS IKM stuff and the VST stuff that I use in Sonar. I would imagine they are transferrable but, an e-mail to IK would probably answer that for sure.
2) I haven't used the iRig or the iRig HD. I have the Alesis IO dock and briefly tried the Apogee One with the iPad. Whatever you buy, make sure it isn't the version that goes in the headphone jack as those have problems with feedback between the input and output channels and general noise.
I did a lot of research and the Apogee Jam and iRig HD seem to get a lot of positive feedback. I chose the IO dock because it had mic preamps with phantom power. At the time I thought it would be nice to have the ipad for demos and sketches. I would not recommend it. The iRig HD wasn't available back then but it can be used as a mic pre amp, as well. Check out the Apogee Jam too, however you will need a Mac to upgrade firmware. Can't be done on a PC.
Also, I don't know if you're aware but you can connect core audio compliant USB audio interfaces to an iPad using the USB camera connection kit. Your Focusrite 2i4 should work. Try that first. Most of the iOS DAW apps (MultiTrack DAW, Auria, Cubasis, etc.) have lists of supported interfaces. The camera connection kit is much cheaper than the iRig HD and can be used for other purposes. The only catch is that your audio interface cannot be powered by the ipad, it will require its power supply plugged in.
3) Amplitube FREE just has less gear but, you can still buy all of the same extras (Fender, Jimi Hendrix, etc.) from the custom shop individually. When you pay for the full version you get 4 amps and a handfull of pedals. I wasn't a huge fan of the Amplitube full version amps. The high gain versions had way too much amp hum/noise for my tastes. I did get Amplitube Fender and I enjoy using those to practise and come up with ideas.
Amplitube can be a bit of a black hole in terms of in-app purchases. You can buy an 8-track recorder, a sequencer, a bunch of drum loops to jam along to and effects for mixing. If you think you are going to use any of those features, post back and I can provide some other suggestions.
I hoped some of that helped with your questions. I have wasted way too much money on music apps for the iPad so feel free to ask me any more questions. One option you may want to consider is the iPad DAW by the name of Auria. You can get a version Overloud's amp sim as an in app purchase. It is, by far, my favorite iOS ampsim and Auria will give you a lot more flexibility for ideas and coming up with arrangements, etc.
For simple practise and sketching don't overlook the GarageBand for iOS. The amp sims are actually pretty good and the app is only $5. It is a little weird as a sequencer but, very good value.