What can I fit in 3 days in Kyoto?

I'll be traveling to Japan in a little over a month and will be stopping in Kyoto for four nights and three full days (I'll be arriving in the evening, likely around 7 PM, spending my first night there, followed by three full days). I'm trying to work out my itinerary for Kyoto and have a whole mess of things I'd like to do, including:

Arashiyama (taking the train ride through the Hozu valley, and the Hozugawa boat tour back, walk through the bamboo grove, and maybe do the monkey park)
Nijo-jo
Kyoto International Manga Museum
Nishi Hongan-ji
Higashi Hongan-ji
Fushimi Inari
Sanjusangendo
Kiyomizu-dera
Heian-jingu
Fureaikan
Philosopher's Path (stopping at Honen-in and Ginkaku-ji)
Shugaku-in Rikyu
Kinkaku-ji
Kyoto museum for world peace
Ryoan-ji
Kyoto Handicraft Center

These are just things I jotted down ages back while flipping through my guide book. I'm not sure what I should make a priority and what I shouldn't bother with, or just leave for next time. At the moment the only things I would not budge on are Arashiyama and Fushimi Inari. I'd love to hear opinions from others who have been to Kyoto on what I should do, in what order. I don't want to plan too much and have to rush through my stops, but I do like fairly fast paced travel. I'm also open to other suggestions but would prefer budget-friendly suggestions since funds are a bit tight. Also, I'm already going to Nara on a separate day, so I don't need to take any time out of my days in Kyoto for that. :)

Thanks for any help!

A walking tour of Higashiyama is generally top of the list in any guide book. It'll likely take you half a day minimum, but cover the best Kyoto has to offer. Start at Kiyomizu-dera and work your way North. If done right you should catch the following.

Kiyomizu-dera (Buddhist temple)
Sannen-zaka (an old street & picturesque district)
Ninen-zaka (an old street & picturesque district)
Kodai-ji (Zen temple)
Maruyama-koen (park)
Yasaka-jinja
Chion-in (Jodo Shu temple)
Shoren-in (Tendai temple)

Another Day seeing Ryoan-ji and Kinkaku-ji is a must (though it likely won't eat up more than half a day).

And finally, a wander through Arashiyama is nice way to round things off, though again, it likely won't eat up more than half a day.

One evening at least you should venture out to Gion and walk through Pontocho, a single alleyway with a traditional feel (should be done at night to get the full effect), followed by Hanami-koji, likely the most famous Geisha district there is, though you'll have to fight the tourist traffic while you're there, as they all scramble for pictures of Geisha.

It is also worth it to hop the train south to Uji to see Byodo-in, for a look at really old architecture, and then hit Inari Station on your way back for Fushimi-inari Taisha. Make sure you walk the whole trail back into the mountains, as that's where the shrine is truly unique. I found most tourists won't walk past a certain point. Once they've got their pictures, they turn around and leave. If you keep walking up the mountain, you'll find you have the place all to yourself, and is more than worth the trek.

If you do not mind long walks, there is a lot that you can fit within three days:
- eastern part of Kyoto from Ginkaku Ji to Kiyomizu Dera and even futher to Fushi Inari and Tofukuji
- Ni-Jo, Imperial Palace (reservation necessary), Kinkakuji
- Arashiyama area
You could also visit Nara which is one hour train ride from Kyoto
Enjoy your trip!

IF you go at a fairly good pace, like walking, and can navigate the bus and subway map, POSSIBLE days are:
AND note: NO input to the 3 museums you mentioned OR the Imperial Villa
1. Sanjusangendo; Kiyomizudera to Heian Shrine;
2. Kinkakuji, Ryoanji, Arashiyama (relatively easy to get to Arashiyama from Ryoanji)
BUT you may not get to do the boat trip and romantic train: to do both of these, AND the sights of Arashiyama itself, would be a full day, thereby taking loads of time away from other possibilities
3. Fushimi Inari then to Ginkakuji, Philosophers Path with Honen In; Handicraft centre

This will nix Nijojo, the Honanji temples, the 3 museums you mentioned & the Imperial Villa

BUT you can't do it all......
You'd need a few more days to cover all of your suggestions

Download the kyoto transport.pdf. and print it in colour: will help enormously
Post if you need more suggestions

id miss out kyoto handicraft centre, my girlfriend found it disappointing as there was alot of mass made things, id do jonny hillwalkers toure as that takes you to little craft shops and to craftmens workshops not usually open to the public , its ?2000 pp and takes about 5 houres to complete, this was our favourite day in kyoto.

If your stay coincides with the 21st of the month, I'd highly recommend going to the monthly lively flea market held in the grounds of Toji. There are lots of interesting fresh produce sold by farmers (fresh fruits, veg, even honey), kimonos, food stalls, tablewares and more! We had a lot of fun taste-testing the different types of preserved fruit & veg, and there's a great overall atmosphere.

Tip- get there early, especially if the 21st coincides with the weekend as we found it became very crowded very quickly!!

See:
http://www.japan-guide.com/e/e3919.html