Ah!
You sure this is a beginner question? :)
Once you've switched to pmode, the value at 0040:006C will no longer be updated by the timer interrupt (you'll have turned off interrupts before the switch to pmode, or you'll reboot immediately - the existing 16-bit interrupt code won't work).
You'll probably want to look at Kris Heidenstrom's timing FAQ:
ftp://garbo.uwasa.fi/pc/programming/pctim003.zipProbably more than you wanted to know...
There's good introductory information (and links to more) on entering pmode, and getting an OS working at:
http://www.execpc.com/~geezerYou might want to subscribe to news:alt.os.development - they'll tell you you've gotta read Tanenbaum and a whole lot more before you even start coding... Neccessary if you intend to write a "Windows-killer", but for an "educational OS", I don't see why you can't "wing it".
Ralf Brown's Interrupt List, besides the interrupt list, includes the "ports list", "cmos list", and "memory list" - you've probably already got that.
The only general hint I can give you is that to read/write multiple-register ports, you "out" the register number to one port (70h for cmos - I think the RTC registers are the first dozen or so), then "in" (or "out" to write) the next highest port - 71h - to get the data. About the only thing I've actually *done* with ports is "beep the speaker"...
You've got yourself a lifelong project there - you'll never be bored again! (frustrated, yes)... Let us know how it comes along!
Best,
Frank