Doing a Clean Install with a Upgrade Windows 7 Version

OK, I've spent several interesting and educational hours going through all the threads I could find on upgrading - and it was time well spent thanks to several very helpful people.

I found most of the answers I needed.

Some still remain, however...

I have an HP machine running 64 bit Vista Home Premium. Got it last June, including the upgrade to Win 7 - which just arrived.

I have done a full backup of the HDD.

From the thread, I gather I have 2 options:
1: Do a true upgrade over the Vista, it will save the old OS in a folder & will register all of my many apps and run them with no problems (assuming compatibility, which has been verified).

2: Get a new HDD (1 TB or bigger), install that in my PC and do a clean install to that blank disk. So far so good - and I gather that when it detects the existing Vista it should have no problems.

Since my current HDD is 2/3 full, I like option 2 - but that would mean having to then copy all the files over with EasyTransfer...and that only copies data files, not exe (app) files, right? I assume then I would need to re-install all of the apps (most of which I have the installers handy, but not all)...which seems like a lot of work.

So, I guess the long winded question is - is there a better way, one that will move ALL the files (data AND apps) to the new disk, and set up the registry to make my life a lot easier than re-installing everything?

Or would I just be better off installing per option 1, and hope there are no problems?

One other quick question -> Soon after I got the PC, it somehow got infected by maleware & spyware...after some really nasty work I think I got it all (Maleware bytes, SpyBot & Windows Defender don't see them...) - but my machine has never regained it's youthful vigor of 5 months ago, sometimes it slows down for minutes at a time...Will doing the option 1 get rid of any residual problems, or do I need to go option 2 to be sure? And is there some wondrous utility that I can use to find out exactly what apps I do have loaded?

OK, that pretty much confirms my best - and worse - expectations...and means I'll need to wait until I can take a few days away from the current project - which has (I hope ) about 2 to 3 weeks left to finish...

Thanks.

Ok - I see posts that are all over thboard on this, but here is my situation:
I had a fully licensed version of XP Media Center that came with my PC
I upgraded to Windows 7
My hard drive failed and I replaced it
I attempted to load Windows 7 from the upgrade CD - never dawned on me that it was ONLY for upgrades
It won't accept my product key at activation
Of course I either don't have or cannot find any recovery disks for the XP previously installed.

I see posts saying the workaround described is not "endorsed" by MS and I want to keep everything on the up-and-up. Can someone advise?

I have a valid copy of Vista 64 bit and also had to replace my 750GB hard drive this week to Frisbee dust! So bought a 1TB to replace it. Amazing what a 4.5 year old can do to a hard drive with given just a few keystrokes! LOL
Well at least I had a back up copy from my Vista OS that installed just fine with the Windows 7 home premium 64 bit, but not so good for XP Pro 32 bit. Just thought I would try it as he crashed that PC as well. He was in the "no internet" so lets fix it as daddy does! God bless the little hacker to be!
After watching my little monsters (like energizer bunnies drinking nothing but power drinks and B12 shots) and trying to repair both PC's, just deleted the windows/system32/config file on the wife's PC.....exhausted...... I was able to get everything back as it was on my PC but the wife lost all her junk files. Darn shame. Look at the extra space.
Well with a clean install all is well. For now.
Actually with what I learned about windows 7 the system runs a little smoother now.

Nice hat brink!

Techymike: If you still have a backup image of XP, it needs a repair install to recover from a HD or computer change.

Boot from the CD, ignore the first R for repair, wait til it discovers the installation and then choose Repair.

It's an in-place Upgrade which only needs reactivation.

There are workarounds if SP's are diff between installation and installer, or OEM vs. retail.

Don't know if this is helpful but I just did one myself so thought I'd offer it.

The back up was from Vista OS. The wife.s PC has XP. Anyways she needed a clean install.