It sounds like you are experiencing a 'runaway application'. Read the following link:
What I suggest you do is when it occurs, open Activity Monitor and take a Screen Shot (COMMAND/SHIFT 4) and then go to the nearest Apple store genius bar with the evidence. Usually these are infrequent and a restart cures it. It should not be allowed to last a couple of hours.
Regarding the trackpad:
In addition to the link, sometimes a very thorough cleaning will restore proper functionality.
The OP explicitly said the *kernel* is taking 300%. I don't think that it is recommended practice to kill the kernel, even if it is a 'runaway' app. I currently have exactly the same problem on my new (one week old) MB Air 4GB 256 GB SSD with 10.7.3 and all other updates applied (including the firmware). A restart did *not* help me. I first noticed the issue a couple of hours ago when the fans started running like crazy during a Time Machine backup. I looked at Activity Monitor and the kernel was at 230%. Once the backup finished, the kernel started behaving again, and so did my MBA. An hour later, next Time Machine backup and the kernel took off again, this time around 270%. And, once the backup was finished, the kernel just stayed there. I restarted (not shutdown/boot, but restart) and the kernel came up at 300% and has been like that since I rebooted. Its been up for 30 minutes now, and the kernel has already racked up 1:30 (that's one hour 30 minutes), so it really is at 300%. It's at about 380 MB real memory, but I don't remember if that is normal or not. But 300% CPU is definitely NOT normal for the kernel.
I don't know how to track this kind of issue down any further than that. My closest Genius Bar is a tad too far away.