Oogie,
Let me take a stab at helping you get at least some of your DAM setup in Lightroom going. As I go through this, please keep in mind that regardless of the system you finally adopt, catching up will take some time. Toward that end, I would suggest you just do a little at a time. Just as importantly, once you settle on a system, make sure that you follow through on any and all new photos as you go. When you add new work to Lightroom, follow all of your procedures on all of the new photos.
Okay, here we go.
I also use a system of daily folders nested inside yearly folders. For example, Monday's shoot went into a folder named 120107, which is inside my newly created 2013 folder. The day folder's name is YYMMDD format. Notice that I leave the "20" off the year. That's because I don't have any photos from 1913, and by the time 2113 comes around, I'll be long gone, and won't be shooting any more. So I save the keystrokes there, only to use them on the month and day -- the month and day must always be two digit numbers or the computer may not sort them correctly. I usually follow the date with a short description of what I shot that day. For example, I shot some portraits that day, so the full folder name would be, "120107 -- Smith Portraits" It's just a way of making sure that somehow, some way, I can always be sure to be able to find my photos. And if Smith ever wants to shoot more portraits, I can find those, separately from these.
As far as collections are concerned, it might be helpful to think of collections by the term most of Lightrooms competitors use -- categories. So you have to ask yourself what categories your photos fit into. I literally sat down with a virtual "pencil and paper" (my work processor), and wrote them out in outline form.
As you do this, remember that Lightroom as different types of collections. There are regular collections, collections sets, and smart collections. I tend not to use smart collections too much, but there may be ways for them to be of help to you. But let's stick to regular collections and collection sets for now.
As I started my list, I realized that I shoot general types of photos, and specific types of photos, and that, generally speaking, many of the specific types fit within some general type. This is where collection sets come into play. For example, I shoot wildlife. All kinds of wildlife. So I have a collection set named "Animals." What kinds of animals do I shoot? Great Egrets, Robins, Grizzly Bears, Squirrels, and a host of others. Well, they are all animals, but the Great Egrets and the Robins are also Birds. So within the collection set called "Animals," there is another collection set called "Birds," and within that is a regular collection called "Great Egrets" and another called "Robins" (along with several other collections for other types of birds). And every time I shoot a kind of bird I've never shot before, I create a new collection within the "Birds" collection set.
Then I have another collection set within the "Animals" collection set called "Mammals," and within that there's a collection called "Squirrels." The grizzly bears go in a collection called "Grizzly Bears," but that's in another collection set called "Bears" (because I also shoot black Bears and Brown Bears, and maybe someday, Polar Bears), which is within the "Mammals" collection set, inside the "Animals" collection set.
In my Library, my Collections ends up looking like this:
Animals
Birds
Bald Eagles
Great Egrets
Hawks, Red Tail
Robins
Snowy Egrets
Mammals
Bears
Black
Brown
Grizzly
Squirrels
Next Major Category Collection Set
Next Sub-Category
Next Sub-Category Collection Set
Next Sub-Sub-Category
Next Sub-Sub-Category
And so on.
Yes, it can get pretty complicated. But it's worth it.
One of the neat things is that although you can't put a photo in a collection set, any photo can be in as many regular collections as you want at the same time. For example, if I want to create a collection for photos I want to print, and I have a photos of a grizzly bear that I want to send to the printers, I can have it in both the "Grizzly" collection and the "To Be Printed" collection. And if I shot that grizzly in Yellowstone National Park, it can be in the Yellowstone National Park collection as well.
Keep in mind that Keywords work in a similar fashion. You can nest keywords inside other keywords. Unlike collections, though, you can have a photo assigned to both the sub-category keyword and the major category keyword at the same time.
Which system you decide to use will depend on how you work and how you see your overall collection of photos. Personally, I use both systems side by side, as I feel like both have their place in my work. You can search keywords, but you can't search collections.
Here's the catch: I shot the USAF Thunderbirds at an airshow. I can keyword those photos using keywords like "Aircraft," "Military," "Thunderbirds," "USAF," "F-16", etc. But if I search on "Aircraft," and I didn't add that keyword to a photo of the Thunderbirds, it won't show up. Your system is only as good as your willingness to keep it up. What are all the possible key words that could apply to a photo? As many as you think of today, next week you'll think of more, and then you have to think about all of your past photos, and do any of them fit that keyword? And all that applies to collections, too.
All of this applies to your historical collection, as well. It's just more collections and/or more keywords. You can set your Library thumbnails up so that they display the file format, which means you'll know if it's the original archival scan TIF or the lower res JPG just by looking at the thumbnail. You can also display any number of other things on the thumbnail as well. Just put your cursor on the border at the top of any thumbnail, and right click (if you're on a PC; if you're on a Mac, it's whatever the Mac equivalent of right clicking is). Be careful exactly where you place the cursor, though. There are 4 distinct places at the top of each thumbnail where you can put info, and each one is set separately. So if you want a specific thing in a certain position, make sure your cursor is in that position when you right click.
You can also have LR display that same info in Loupe view. That setting is accessed through the View menu at the top of the screen.
To link the different versions, you could just stack them. Decide which thumbnail you want on top, and click on it. Then, holding down the Ctrl key (Option on Mac), click on the other versions one at a time. When you've clicked all the versions, hit Ctrl (Option) G, and they will be grouped into a stack. A number will appear on the stack's top photo telling you how many photos are in that stack. On each side of the thumbnail, there will be two short vertical lines. click on one of those, and the stack will open up so you can see the other photos in that stack. You can then do anything you want with any of them (print, edit in Photoshop, whatever). When you're done, click on one of the vertical lines again, and the stack will collapse. The help file will tell you how to add or subtract photos from an existing stack.
I think, though, that one of the things that beginners have trouble getting used to in Lightroom was something that took me some time to get used to myself -- the fact that we no longer need many copies/versions of the same photo. You say you have original archival scans as TIFF files, the lower resolution JPG reference files, the even lower resolution web files and tiny thumbnails. You don't need all those versions with LR. All you need is the original TIFF files. Lightroom will create its own thumbnails. When you need low res web files, use the export feature. Once you set that up (and there are excellent tutorials out there on how to publish to the web directly from LR), that's all you do. The low res versions will go to the web, and never actually exist on your computer. So you don't have to keep track of all those versions any more.
Like your friend, I shoot RAW, and I do 90% of my processing in LR. So I take a RAW photo to the Develop module, and work on it. If I decide I want to try something different later on, I just make a virtual copy, make the new changes, then stack it with the original. Since LR doesn't actually change the original photo, it's still there, but I no longer have all sorts of versions and variations floating around.
Hope this helps. Have fun.
Don