Bali will be lovely in July. With two weeks, you can spend a week on Bali, perhaps in two different hotels (one by the beach, one inland near Ubud), make a short stop in central java to see Borobudur and Prambanan and have a few day stopover in Singapore. You really don't want more than 4 atops in two weeks, otherwise you'll feel like you are spending all of your time in transit.

I don't know what kind of special fares you might find, but I would say that it will be hard to get business class fares plus all of your honeymoon accommodation for that price.

I agree with Kathie that you will not be able to add in business class fares. Personally, I don't see business class as worth it - I'd much rather fly coach and spend $$ on hotels, food, gifts...I'm also 5'2 with a narrow frame.

That said, I'd definitely spend a week in Bali, agree to split your time between the beach and Ubud. There is a lot to do in Bali, it's much more than the beach. We really enjoyed climbing Mt. Batur to see sunrise, and liked that in Bali one day you could climb a mountain, the next go biking and see temples, and then lie on the beach and drink cocktails the following. As for hotels, the beach hotel I stayed in and recommend is within your budget - the Alila Villas Soori. If you want a secluded, quiet few days the hotel is perfect. Amazing villas and the only hotel for miles and miles on a pristine black sand beach. REALLY black sand- not dirty brown like I was expecting. If you want downtime it's the perfect place. On the flip side, it's at least 30 minutes down a narrow, not well paved road to get anywhere else, so you need to know what you are getting into. The food is some of the best I've had at a resort anywhere so I didn't mind having dinner there more than once.

Bali will be in dry season, not so sure about Malaysia.

I agree with both comments -- Bali, Central Java, Singapore make a great 2 week trip.

I'd choose Singapore Airlines and connect to Java or Bali from there. Within Indonesia I like Garuda or Air Asia.

I'm in agreement -- fly coach and spend your money on the ground. Many airlines have enhanced coach, e.g., executive economy.

You'll have good weather in Bali and Java in July. July is the beginning of the high season in Bali and rates go up. Business is weak this year so you may be able to get a deal. A few days in Ubud are a must. For the beach I like Seminyak.

These are some honey-moonish places in Bali that I'd recommend. Some are quite price, some are good values.
Ubud: Como Shambhala, Alila, Samaya, Kayu Manis
Seminyak: The Legian (the one in Seminyak), Samaya, The Colony.
East Coast: Amankila

There are also zillions of villas in Seminyak, not right on the beach, but close. Take a look at the Laksmana group.

In central Java if you can afford it, go for the Amanjiwo. It's extraordinary. Be aware that Ramadhan, the fasting month, begins July 9. This will impact your experience in Java -- and parts of Malaysia. Not so much at resorts, but in the general community.

The only thing about Bali is that you won't find that kind of "tropical paradise" beach, i.e. white sand, turquoise crystal clear waters etc. Something like this, to make an example:
http://www.molon.de/galleries/Malaysia/Sabah/Sibuan/Island/

That's not available in Bali.

If you are interested in good snorkeling from KL you can fly to Redang Island in 50 minutes ($160 RT) and find resorts with beaches and the marinas will take you our to the reefs for snorkeling.. In KL the city is not that interesting. I spent one productive day And then headed for the awesomesome Cameron Highlands, 2+ hours from KL for 2 days in mt midst of the tea and flower plantations.
In Bali I always gained more information with insights from a guide for 1-2 days. We used a fello named Putu also referred to as Balifriend. He charges $65 for a 10 hour day.

Thanks all, this is really brilliant stuff.

Very much appreciated.