Hi
You really don't need to do a 'tour'. I know some like tours, and it is very much a personal choice.
personally I can't stand organised tours and prefer the great public transport system and tourists bus services, cheap too.
The monorail and train is a really easy and cheap way to get about and many stops are near the popular sights or connections to the trains or buses http://klcityguide.my/kuala-lumpur-train-map/ http://www.ktmkomuter.com.my/station_maps/routemap/kl-transit-map.pdf http://klcityguide.my/kuala-lumpur-train-map/ http://www.myrapid.com.my/ http://www.ktmkomuter.com.my/index.php
There is a ‘free’ bus doing the sights http://www.gokl.com.my/getting_around and http://www.malaysiafreebies.com/go-kl-city-bus-free-travel-kl-route/ is a useful link, plus they do have a facebook if you search GO KL (Kuala Lumpur City Bus)
There is also a hop on hop off tourist bus that covers most of the sights, you pay for a 24 hour or 48 hour pass http://www.myhoponhopoff.com/
Know what you want to see. Get a decent map. You can cover most using public transport.
look at the green banner at the top of this page and check out the ‘Travel Guide’ [in the MORE tab] and ‘Things To Do’ tab [ http://www.tripadvisor.co.uk/Attractions-g298570-Activities-Kuala_Lumpur_Wilayah_Persekutuan.html ] which list lots of pointers of what to see and where to go as well as other information like restaurants
http://mappery.com/Kuala-Lumpur-Tourist-Map a half decent map is a must when planning, http://www.tourism.gov.my/en/Master/Web-Page/Footer/Resources/E-Brochures has some great leaflets with maps, especially the one called Kuala Lumpur Malaysia's Dazzling Capital City http://corporate.tourism.gov.my/images/Maps%20of%20Malaysia/map_Selangor_KualaLumpur.pdf
http://www.tourism.gov.my/intl_en/places/state_list/kl
Batu Caves is doable by taxi or train. Not a fav of mine - great from the outside, but once you have climbed the 250+ steps it is just a dark smelly cave. The easiest way to get to Batu Caves is probably a taxi at around 50-100myr each way depending on the type of taxi you get, but you can get there by monorail and then train. Batu Caves station on the Sentul / Klang KTM line, will probably take 2-3x in time but will be a fraction of the cost. If you find nearest station to your starting point, then find Batu Caves http://www.ktmkomuter.com.my/station_maps/routemap/kl-transit-map.pdf http://klcityguide.my/kuala-lumpur-train-map/ http://www.myrapid.com.my/ http://www.ktmkomuter.com.my/index.php
Taman Negara is NOT a day tour. You really need at least 2 nights. Taman Negara is a long 4-6 hour drive north from Kuala Lumpur, it is 175km from Kuala Lumpur to Jerantut, and then it is another 68km to Kuala Tahan, the gateway to Taman Negara. Kuala Lumpur to Jerantut by Perwira Ekspres 4 buses daily, then taxi to Kuala Temeling Jetty