If lightroom works the same way as Adobe Camera Raw try doing the editing to the raw images in lightroom first before you stich them all together. With CR I select all the raw images and so make the same changes to all at the same time.
Not sure what stitcher is? Is it the overpriced software by Autotdesk?. Have a go with
PTGUI Pro (there's a free demo version) and see how that workflow is for you. I've used it for years and would be pushed to switch to anything else. It stitches raw images also but I like to convert to tif first. There's also a yahoo Group called PanoToolsNG that covers ptgui and a fair few posts already there for lightroom.