What to do about VR6.... any help?

My girlfriend's Corrado SLC has been making a great rattling noise when started and still doesn't seem to quiet down all the way after a while. I thought maybe just the chain guides and tensioner but she ran the thing almost out of oil back in the summer so I'm worried that something else could be damaged. She is getting a promotion and being moved to another office which will be an hour drive each way, and my cabby that she has been driving won't cut it for that drive each day. She says she can't stand the wind noise... OK, her company was going for a company car but it looks like they will flip the bill to have her car fixed. The dealership said that for the price to get new parts for it and labor to take it apart and re-assemble it might be cheaper to get a new engine.....hmmm.... The car has 100,000 miles on it now. It runs alright and seems to have all it's power.
How much does a whole engine run and where is a good place to get one? Dealership said we would be better to get one ourselves. If we just have it repaired what all should we have done when this thing is opened up?
I don't have much time to check all this out so everyone's help, well it will really help.
Thanks very much