[HD2 General] sean is here.:
You kinda need to define what you mean by "clean"...I assume you mean stock (and never been modded, but these are 2 different things totally unrelated to each other, more to that in a minute).

IMO the best thing you could do would be to read up on the flashing process. This will tell you what to look for, if you're looking for a stock never-been-modded phone.

But back to your question...the first major sign I'd look for would be HSPL. I'm not going to go into detail about how to find out if it's installed. You'll have to do your own homework. Read every 'how to' and 'newb' (or noob) guide on xda. XDA is an awesome site and the dev's here write awesome documentation. Do them the favor of reading it. I mean, I don't know what you're an expert on but it might get on your nerves if I ask you simple questions about that topic cause I'm too lazy to do the research myself. The research is easy, the reference material is all contained here in various forums, depending on what you want to do. I show my appreciation for that by taking advantage of it, and don't forget to thank the dev's if something is especially helpful...they like that. :-)

As far as checking to ensure that it's still running WinMo...that's gonna be about as effective and informative (about the phone being virgin-stock) as whether or not it's raining that day or not. What's that got to do with anything? Exactly. Nothing. My HD2 is running (at the moment) a WinMo 6.5 build. But it's been flashed more than a hundred times. My daily software is an SD Android build. Before I flashed my HD2 for the first time, I probably spent about 30 hours just reading about the process and trying to understand the process of what I was going to be doing (while reading, I usually had video tutorials playing on my 2nd monitor...I'd give up the reading when it got interesting). So that's it, really...read read read. It's not fail safe. I can't tell you how many times I waited on pins and needles to find out if I had ****-canned my new €400 phone. If you have a heart condition, you just shouldn't ride this ride. ;-)

I just got a SGS2, cause I prefer Android to WinMo. WinMo's a full time job, as is flashing. Something was always not performing the way I wanted it to (efficiency or performance etc), which was why I started flashing, but it gets to be like a drug. Nothing's ever good enough, cause you wind up wanting the best. I'd flash a ROM and install all my **** (manually, one cad file at a time) and then flash a different one and have to reinstall everything again. It was even worse if I had set up my homescreens, and folders the way I wanted them...to that end, I'd highly recommend that you also research mass-installer programs. I can't think of the name of it right now, but you pack all of your cad's in one folder and this program installs all of them (which means like 65% typically, cause invariably about 1/3 will fail for one reason or another).

Even still, looking for HSPL (which is required to flash anything on the HD2) is not very indicative as to whether or not it's been previously modded. When I got my phone it was virgin/stock, of that I'm sure. I bought it from a person, and the person was not capable of performing such tasks (he wasn't so technically inclined). But in your case, you're going to have no idea. It is not only possible but also very easy to return the phone to stock by removing HSPL leaving virtually no trace of it having ever been modded (I say virtually, cause I don't THINK that it can be traced when HSPL has been removed, but I'm not a dev and not a guru). So even the absence of HSPL doesn't even really tell you that it's never been modded, it only says that if it was- then the modder was smart enough to cover his tracks.

Basically, I don't think there's an answer to your question. There are clues that say YES THIS PHONE HAS BEEN MODDED. But there's no definitive sign to look for that say THIS PHONE HAS NEVER BEEN MODDED, and you dunno if someone's gonna lie to you. But I am inviting you to prove me wrong, read the documentation and get back to me.

Good luck flashing, don't **** it up though. You'll be pissed if you brick your ****, which is easy to do. Hell, it's probably a thousand times safer to buy a phone with HSPL installed, then you can flash all you want with no risk. The main risk, is ****ing something up in the HSPL installation process, but there are ways to minimize the risk...which all amount to: read, read, read.

And if you decide you'd be interested in previously modded HD2 (with HSPL already installed), let me know, make me an offer. Mine's just a wifi media device at the moment and I'll probably be marketing it in the near future regardless. It currently has HSPL, and I haven't decided to remove it before sale or not. I saw one on Amazon last week that was at a premium price, cause the seller had Android running on it. It's a great phone if you like WinMo, but I find Android to be much less 'high maintenance' and I used to be a huge WinMo fan (I'm a 10 year WinMo user, if you can believe that!).

Regardless, this is getting long. Those are my 2pence. Be easy.

[EDIT] Hell, if you were closer I'd let you borrow mine for a few weeks to see if you like the phone. I'm a nice guy like that.