Converting RAW files? LR or ViewNX?

Do it this way, do it that way. I could tell you ten ways to do it. But the general preface is that working with the RAW file itself allows you greater latitude since you have more information to manipulate. Do as much as you can with the RAW file before exporting to Jpeg, and eliminate any unnecessary steps along the way. If you convert to Tiff only to edit further when you could just continue to edit the RAW files you're adding time, adding a step that could introduce (amplify actually) noise, and you'll eventually run out of disk space.

I don't work with LightRoom, but I think that it doesn't actually write over the RAW files, but rather saves the recipe that was used on the RAW files. So with that being said if you shoot in RAW you'll not write over the original. You can see why this is a good thing with what you went through already.

General rules of thumb:

1) eliminate noise first, possibly after bringing levels and brightness up but you want to kill noise early on.

2) sharpen last, well sharpen before you downsize if you do downsize. The program that re-sizes the image will try to make it look as sharp at 1000 pixels wide as it does at 3000 pixels wide, so sharpen before resizing. If you don't re-size then sharpen last.

2-1) Correct for distortion BEFORE you adjust for tilt BEFORE you crop.

3) Don't go nuts with the contrast. That's not to say that you won't apply it heavily at times, just don't' get into that garish look. Watch for banding.

4) Don't delete your RAW files.

5) Jpegs aren't bad, they aren't evil. Most of the stuff you see on the web is a jpeg, most things printed are jpegs, and most that isn't' a jpeg when you upload to the printer gets converted to a jpeg by the printer so they can print. Use Tiffs if you really need to rescue a severely lost cause with something, otherwise Jpegs are adequate for just about everything including general edits. Just be sure to save Jpegs in an uncompressed form, or 100%, or whatever Lightroom says. I use Tiffs about one half of one percent of the time. It really is that unnecessary.

6) Go with what works right with your brain. If CaptureNX is more intuitive to you than LR then by all means use it. It's the image that counts not the process to get there.

7) Just about any plug-in that's offered for sale can be replicated by yourself. Don't go thinking that you can't achieve something that's for sale just because they say so. On that note, many products offer automation to do things and it may be worth it to you to buy that product. Something like a plug-in that enlarges the file to gargantuan sizes can be replicated to the point that you won't be able to tell which was the bought plug-in and which was the one that you just worked over, however you'd spend half an hour working one file over where as the plug-in would just take seconds.

Keep it simple

Don't buy anything you don't need

Take it slow

Kill noise at the start, end with sharpening

Try to do the same thing and analyze each step.

When you complete your editing process(es) do you remember to sharpen the image as the final process before saving the image ?