How can I get Lightroom to download all photos on my turnkey computer afterwich upload w/o long wait

Question

I have a turnkey desktop computer dedicated for photography and video use only.  Below is a listing of tech points about the computer.  I operate with Adobe Creative Suite 6 Master Collection.  Also installed is Lightroom 4.  I played around with the latter and immediately could appreciate how the software will expedite a lot of the work on photographs.  But, and this is a big one, after following through on the advice from several on-line "experts" by having Lightroom incorporate all the images on the computer into the Library, afterwards I could no longer bring up in Lightroom a photo to work on without having to wait ~3 to 5 minutes for each photo. 
At some point I counted the number of images on my computer, can't remember how that was done but anyway, about 40,000 keeps coming up in my head.  I'm not absolutley sure but it's safe say there are a lot of photos on the computer.  My plan is to search through these photos and categorize them under subjects/ideas using Lightroom while still keeping my current filing system by year, month, day and subject.  Additionally, in the past few years I have been shooting a lot of RAW images and I believe using Lightroom would help me be more time efficient with any editing needed.
I don't have a lot time/patience to play around with "possible" solutions, but am willing to try someting that has been known to work in cases like mine.  At the same time, if my computer set up and/or the number of photos I have installed is prohibitive for Lightroom to operate efficiently, I would be disappointed to hear such but just the same would be very appreciative to know in advance of further futile attempts.
Thank you for your time and consideration,
Baker
Computer:
Intel Core 2 Quad Q6600 2.4 GHZ LGA 775 Processor
EVGA GeForce 9800 GTX 512 P3 N871 AR  Video card
Windows Pro 7
Antec TPQ-1000 Power Supply
4 x 2G/Wintec 3AXT6400C5--2048 memory
3 x 1T/WD 32m SATA2 WD1001 hard drives

Answer 1

Rob,
If I understand you correctly, a “bad” photo file will create problems for Lightroom that could include long delays when bringing up any image in the catalogue.  So I should do the following:
1.       Start over with a new catalogue.  I think I am in that position by default more or less because I could no longer work with any images in Lightroom until after I deleted the catalogue which incorporated all of the images on my computer.  It just would not work.  Now Lightroom works again but with one folder (a photo shoot) at a time.
2.       I have images on two 1 TB hard drives.  Not sure I could get all onto one hard drive. (suggestions)
I was under the impression that Lightoom would search the entire computer and only pull photo images into a catalogue.  Is it possible that Lightoom would include video files?  I could put all photo images on one hard drive into one folder.  That would separate the images from video files.  But in the Lightroom cataloguing process, must I direct the process by indicating which folders are to be included in the catalogue?
3.       All my current folders are by year, month, day, and event.  However, the numbering system for my Nikon cameras goes to 9,999 and then starts over at 0001.  Also, I use two cameras.  And, as newer/better cameras became available, I switch cameras.  So the number 0001, for example, has probably been used a number of times since I first started using digital.  All images are unique within a particular unique folder, but it would be a monster job locating all images with the same number.  All folders are unique, but I’m pretty sure there are duplicate numbers among images files.  And in some cases, there are duplicate images (with the same image) in different folders.
4.       Does the presence of duplicate images or image numbers in separate folders mean I can’t expect Lightroom to function efficiently?
5.       Is there a step by step process I could use that would allow me to bring in a year’s worth of unique folders containing images at a time, so I could test Lightroom to see if it has been adversely impacted?
6.       I’m not familiar with third party renamers? 
7.       I would be lost if I had to let go of (rename) my year, month, day, event organization.  I was hoping to use Lightroom to gather from these individual dated folders images I found that fit some theme such as weather, Northwest sports, nature shots, etc., without eliminating my current filing system.
Sorry for responding with so many questions.
Thanks for the time and consideration.
Bakerrr