First off:
http://www.windowsnetworking.com/articles_tutorials/Deploying-Windows-7-Part1.html
That guide is awesome.
2nd: What method of deployment are you using to get the initial winpe image out to the machines? I use WDS and its pretty much flawless. Unless the environment you're in can't handle large amounts of network traffic (which you could use multicasting to help mitigate), I would do it this way.
Which issues in MDT were you having? The only major issue I was having with deployment is where if you go to deploy on a machine wher MDT was used previously, it failed out. I solved this by editing the litetouch.vbs script, right in the beginning, have it delete the c:\_SMSTaskSequence and C:\MININT directories. This will get it to do a clean install.
Other than that, therres really two ways of doing this: You can have a standard image, with everything on it already, and use that to deploy, OR you can have just a stock image (or close to stock, more on this in a minute), and use the application deployment to install apps, updates, etc, all from a stock image.
On our MDT, we have two basic types of installs. I work for a 3rd party IT company that has a few different parts of our business. As we do a lot of hosting in our in-house datacenter, we deploy servers on a daily basis. Because all of these need completely different software, configuration, etc, the only thing I do with the server images is once every 6 months or so, run a task sequence that deploys the image, updates it fully, and recaptures it. No software, no configuration. This allows us to deploy images much faster when we actually have work that needs to be done. I also do this with consumer OSes, only to a lesser extent.
The other part of our business deals with an internally developed piece of software. We sell the software to our clients, and the software comes with a laptop and some various peripherals. Because the laptop is always the same model (or very close), we've created an image that already has all of the software installed (including things like SQL Server, Office, etc), and when we onboard a new company, its as simple as opening up the boxes and plugging in a network jack.
The portion that I haven't looked at yet, but am planning on doing so in the next week or so, is getting the SQL Database hooked up to MDT. This would allow us to install a certain image based on say, the make or model of the computer that is connecting to MDT, or by the username. Thats the next step, and its a pretty big one
Anyway, I'm rambling. Any of this make any sense?