peninsular malaysia 3 year old in tow

I think the East coast should be OK before November? West coast should be the end of the wet season so you might be ok - one big shower a day but you can still do stuff (although my friend in penang recently complained of 5 days of solid rain).
We did a loop of Malaysia with our 6 & 3yr old. We flew into KL, then got a bus straight up to Penang. Hung about in Penang for a week, then got a ferry to Langkawi. There is a lot to do on both islands but the beaches are better in langkawi & the beer is cheaper. Then we went back to Penang & hired a car. With our car we headed East for 3.5hrs to Royal Belum State Rainforest, so a bit of walking/boat trips. Then another 3.5hours East to Kota Bharu (fishing village, museums, craft villages), then an hour south to Kuala Besut and an hour on the boat to my favourite place in Malaysia - Perhentian Islands. We ended up spending 12 days there! From there, we went inland to the Cameron Highlands - my daughters who are never, ever travel sick vomited once each (one on the way up & one on the way down). the road is very twisty! In the Cameron Highlands we visited Tea plantations, strawberry farms & butterfly gardens, before heading back to Penang.
Here's a link to the Malaysia bit of the blog - it's not proffesional at all, just to keep in touch with the kids grandparents, but if you skim through it, it should give you some ideas of things to do with kids.
http://guestfamilytravels.com/category/malaysia/page/7/

Some friends of ours have their blog with a lot more info. than ours and it's more designed as a travel guide, so this might help a bit more;
www.ourtravellifestyle.com

I would second the Perhentian Islands,we spent 8 days there in early July,just beautiful,also The Cameron Highlands were worth a visit.We did venture to Taman Negara but I would give it a miss,Happy travels,it's a great country.

We spent a month in peninsular Malaysia last year mid Sept to mid Oct. We also loved the Perhentians although you may be cutting it fine timing-wise with the start of the wet season. We were there for the last week of September and had perfect weather. While there is not alot to do on Perhentian, my then 4 year old daughter just loved the beach after the hustle and bustle of KL. Swimming and sandcastles kept her happy all week.
We also went to Penang and Langkawi. I think the west coast beaches do not compare but as you said there is more to see and do in these places. The wet season on the west is not as extreme so even though we had some rain (mainly at night) it did not stop us from doing anything. My daughter found the heat a bit overwhelming so we made sure we stayed places that had a pool so we could balance the sight-seeing with relaxing and fun for her. Things she liked in Penang were rickshaw rides, Kek Lok Si temple, fruit farm and butterfly farm.
I know you said you prefer overland, but Air Asia offers cheap flights. You could fly from KL to Kota Bharu for the Perhentians then after the island get the bus from Kota Bharu and head west to Langkawi/Penang and then bus or tain from there back to KL (or maybe you can leave directly from Penang to where ever you are going).
We had planned to visit the Cameron Highlands but decided against. After hearing about the twisting roads as previous poster mentioned, we decided it wasnt worth putting our daughter ( who does get car sick!) through it.
Enjoy your trip!