http://www.daigoji.or.jp/index_e.html

and here:

http://www.japan-guide.com/e/e3916.html

It's rated a 4.07 out of 5 by site users.

The complex is rather large, and there are actually 4 parts. There is the garden (Shosoin), the museum, Shimo-Daigo, and Kami-Daigo. To see the garden and Shimo-Daigo, I would designate 2 hours. If you are going to see all 4, then I would make it a half-day trip. It is one of Kyoto's world heritage sites, but one of the lesser visited ones, so it is not so crowded normally.

Daigoji is best reached by subway.

I plan to spend the whole day in South Kyoto.
Visiting Fushimi Inari Shrine, Byodoin in Uji and the Daigoji Temples.

What is the best route to visit this places as they are all far away from each other?

These sites are not so far apart, actually.

Whether or not you can add other sites to the list will depends a lot on how thoroughly you want to see them.

For example:
-At Daigoji, do you just want to see the temple complex or do you want to see the garden and museum? (or a combination of 2) You can spend 2 hours there just seeing the temple and garden.

-At Fushimi Inari, do you want to just see the main shrine and some of the torii gate rows or do you want to walk the entire path up the hill/mountain? If you want to see everything, it is probably a good idea to assume you will spend 2.5-3 hours there. If you just want to see some torii gates, the shrine, and then head back to the station, you may only need 1 hour or so.

-Byodoin includes the temple and temple musem. How long it takes to see everything will depend on whether or not you want to enter the temple, and when the next available guided tour begins (you must sign up for a time slot after you arrive in order to enter the temple. Otherwise, you can walk around it.)

I would probably not plan much else.

You will need to take the subway (Daigo Station) or bus to Daigoji Temple. Uji and Fushimi Inari can be reached by train on the Keihan Railway or JR Line.

There are a few ways you could do this, and since the trains/subway overlap, for time constraints, I would see Fushimi Inari last, because it does not close.

I want to take my time visiting this places, because the other 2 days in Kyoto will be quite rushed.
I guess I'll easyly spend 2-3 hours in Daigo-ji in the moring.
I'll head to Byodoin next, do you know the schedule of the guided tours in Byodoin? Are they held in English as well?
Maybe I'll stay there for awhile as Uji has some other nice places to visit.

Anyways, Tofukuji Temple is a large complex, but many of the sub-temples are not even open to outsiders, so for visiting the main temple (and the accompanying museum, if you wish), I think you will need at least an hour. It may also be crowded, because it's a popular place to view the autumn foliage.

I think you could see these 3 sites from Osaka, but like the above itinerary, I would recommend trying to arrive early at the first destination.

If you use Keihan Railway, both Tofukuji Temple and Fushimi Inari are accessible on the same line. As stated above, Daigoji can be reached by subway or bus from Rokujizo Station. I would probably visit Fushimi Inari and Tofukuji as a set, since they are so close.

Daigoji Temple is one of my personal favorite temples, so I like it when others go, too. I think it's much more popular with Japanese than foreigners. When I was there, I was the only non-Japanese.