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OK, I got a new 80 GB HD to replace my 40. My 40 had 2 partitions with Win98SE on part 1 and WinXP on part 2. What I did was partition the 80 in 2 parts, formatted them and then proceeded to copy all the files over from the 40 to the 80. I did the win98 partition in XP and vice versa and I didnt get any transfer errors (and yes hidden files were set to show all).

Now, when that was done, I took the old 40 out and put the 80 in alone. First all I could get was my old Win98 would only boot, no boot loader... after I fixed the boot sector with the XP cd, I cant get 98 to load, and then when I try XP, I get some license error... some checking on the net shows that xp thinks its on a different drive letter and it wont load, when scandisk starts it says checking drive G when it's supposed to be D... really frustrating, i'm back on my old HD right now.

I guess copying the files over within Windows is not good? Do the boot files not copy over properly? Gonna try it all over again tonight with this WD tools floppy I have, it will copy data over in a pure DOS mode (bootable floppy disk) so that "should" work... just wondering if any else ran into something similar or knows why I might be having this problem.

Thanks for reading all of that...

Basically what happened was that just the files were copied over (and may not have been all files) and no boot info was copied. Use a program like Ghost or Drive Image or Drive Copy or Clone. Also some manufacturer's utilities include such programs. I know Western Digital does for sure.

OK, I used the WD data transfer tools to do the 1st partition (took frickin forever), and not wanting to wait for the 2nd partition knowing I already copied those files over anyway, and since the 1st had the boot info, thought I'd just try using the new HD again... Well, I got the boot loader to come up, but XP gives me the same damn error and won't load, not even into safe mode. The error is: "A problem is preventing Windows from accurately checking the license for this computer." This is all I could find on it: http://www.jsifaq.com/SUBJ/tip4600/rh4684.htm
but considering I can't even get into XP I can't fix the drive letter problem. Does this have something to do with Product Activation since I changed some hardware? It's XP Pro (the one that you don't have to activate *cough*). Oh and now Win98 won't load using the boot loader... sigh.

So do I have to clone the 2nd partition too? If this doesn't work I think I'm going to have to re-install everything, something I REALLY don't want to do...

You'll have to edit the boot.ini cause it lists the OS via HDD/partition numbers.
Just copy/paste your boot.ini in here and I can fix it for you so you can copy/paste it back, it's a lil complicated to explain how the boot.ini is setup.

EDIT: I just wrote an example boot.ini so you might get the idea. There's an old one that puts Win98 on C: and XP on D: PLUS a new version with Win98 on D: and XP on C: , you'll notice the difference in the partition numbering.
Don't forget that you also need boot.ini / ntldr / ntdetect.com on the new C: , they're on the old C: since they have to be on the bootpartition.

old:

[boot loader]
timeout=30
default=multi(0)disk(0)rdisk(0)partition(2)\WINNT
[operating systems]
multi(0)disk(0)rdisk(0)partition(2)\WINNT="Microsoft Windows XP Professional" /fastdetect
C:\windows="Windows 98"


new:

[boot loader]
timeout=30
default=multi(0)disk(0)rdisk(0)partition(1)\WINNT
[operating systems]
multi(0)disk(0)rdisk(0)partition(1)\WINNT="Microsoft Windows XP Professional" /fastdetect
D:\windows="Windows 98"

I knew I forgot something .... XP (2000/NT4) does not allow to change the partition letter so it might not work when you move it to a different partition.
Just copy C: to C: and D: to D: when my boot.ini edit won't work with XP.
Lemme know how it works.

Thanks for the help Doc, but my problems ran deeper than just the boot.ini. Like I said, WinXP thought it was on drive G and would just crap out giving me that error I stated above. What I tried next was to put my new HD as the master and the old one as slave and guess what? It booted OK! WinXP kept the drive letter assignments of my old drive as C and D so the new drive was F and G. Well now I could finally fix things by doing this: http://www.anandtech.com/guides/viewfaq.html?i=108

I then took out the old HD and now all is finally good!

Thing is, WinXP loads fine but when I try Win98 I get non-system disk or something for some reason... not a huge deal as I very rarely load it up anymore, but it would be nice to get it back. Here's my boot.ini that worked just fine before:

[boot loader]
timeout=15
default=multi(0)disk(0)rdisk(0)partition(2)\WINDOWS
[operating systems]
multi(0)disk(0)rdisk(0)partition(2)\WINDOWS="Microsoft Windows XP Professional" /fastdetect
C:\="Microsoft Windows"

That "S" is actually on the same line but for some reason the formatting here makes it on a new line and I can't fix it, wtf?