When Charity Corner comes around again, you'll have the opportunity to purge your safety deposit box, which has been a helpful event against my hoarding tendencies. My brain doesn't like the idea of throwing out stuff that could be useful or valuable which leads to having thousands and thousands of items in the sdb. I was able to donate 5,000 items over the last few charity corners without having a mental breakdown by using the price checker tool. You've discovered by now that you can't dump the html source of all your items into the tool at once. Here's some tips that helped me stay sane.
go backwards - when you have 10, 20, or 50 pages worth of inventory, you're going to be doing a lot of cutting and pasting into the pricing tool, so it's important to not do it more than you have to. If you start at the first page, any time you move an item to your inventory, an item from the second page moves up into the first page. After a few items are moved, that first page will have changed enough that you'll have to cut and paste the html into the pricing tool again. If you start on the last page and go backwards, all those items that you move only affect the pages you already processed.
break it up into smaller bits - nobody has time to actually inspect 25 pages of items in one sitting. Ideally, you'd do a page or two and walk away, but how do you remember where you left off? Using categories like books or toys, for example, lets you break up the pages into smaller amounts. If you only have 3 pages of gifts to cut and paste, it's a conquerable task. Once you process a few categories, it may reduce your overall number of pages to something you're comfortable dealing with (backwards, of course).
Go for easy victories early - you've probably acquired hundreds of healing potions or omelettes along the way. Definitely deal with them first. Donating or discarding 100 jellies doesn't reduce the number of items in a page, but it reduces the overall total, and that will make you feel good.
I realize that this doesn't directly give you a total or show you what is the most valuable items in your hoard, but the process of cleaning the SDB will show you the valuable items as you go. And once you've purged a few thousand things, those valuable items will be easier to find later.