Thank you all. I am just waiting for some warmer weather to get back into this but I had a few questions.
1.) What do you recommend for gear oil as I'm not sure what the dealer had put in it since I bought it at a Lexus dealership I'm just going to drain it.
2.) What's the best method to inspect the shift linkage as I couldn't see anything wrong underneath when I inspected for leaks.
3.) What could of caused the loss of transmission fluid if I don't see any leaks?
4.)I'm also at 105,000 miles so what service should be done such as timing belt, tensioners, and the like as this is my first car that isn't from 1990 or earlier?
5.)Lastly I just read Brendan's STI 6MT Swap and feel inspired to try it if it's a transmission failure as the trans has always had a certain noise that bothered me and was making funny noises every so often for a month before this when I would drive it. So the question is what's the better option if I don't have the skills, space, or tools to do most of that swap myself?