Great Stuff! I also am running Myrrdrak's conversion, and I even helped him with one of his maps here http://www.cartographersguild.com/vi...unter-map.html that he commented on. We are two-thirds of the way through H2 at the moment, but as I will be skipping very fast through H3 we'll be moving onto Trollhaunt Warrens soon enough.

You'd be surprised at how big a map you can upload on these forums. Save your map as a jpg at 85% quality and I bit it will fit here as a normal attachment with no visible loss of quality.

One thing I have been trying to figure out is how to do proper shading to signify either a slope of height change. In the linked map (it is too big to post as an attachment.) I have many rock walls and some raised sections in contrast to the rest of the elevation on the map, particularly at the very top right, where an altar is situated on top of a raised section. How can I get a more realistic feel to these parts? I think the map looks ok as it is, but my inner self keeps telling me I can do better. Any help would be appreciated
This is just shading and shadowing. I scribbled with a black brush on your map here and you can see what I mean. I added some crude shading to your objects - it will be easier for you because you can place the blackness below certain areas. In general, it would be easier to show the slope if you did away with the rocky area completely and just used black on the yellow floor to show the slope.

Click image for larger version. 

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Also, when I add objects to my image in photoshop, each individual image gets placed on it's own layer, is there an easier way to do this? It is a slow and tedious process.
Probably not. Just merge all the layers into one layer after you insert the images. Also cut and paste images if you are reusing the same one.

One more tip: darken the cavern walls considerably. They'll look much better and the floors will really stand out. Also your grid is very heavy (make it a bit more delicate) and place it over the floor but below the walls and below all your objects.