Hmm, I see you're still bound and determined to stick in two different beach locations, what can I say? I already outlined my thoughts in detail further up-thread about too much moving around. In a more general sense, all you need to book (doable yourself) are the internal flights and the hotels...maybe splurge and let hotel car pick you up at airports. Since it's peak season, only a couple of things need some advance arrangement--such as Sea Canoeing in Phang-Nga Bay (far more interesting, scenic, and fun than the Phi-Phi thing) and the cooking class, both of which can be done directly with providers via internet. I've had multiple great experiences with one of the originals, Chiang Mai Thai Cookery School. Any hotel can book you a spot on the dinner/shows and call you a taxi. Any local agent can provide any service to anywhere you want, on the spot or with 24 hour notice. Some activities like this particular tourist trap Meo village are complete wastes of time. The Night Safari is quite controversial but if that's the kind of tourism endeavor you wish to support, it's your choice. The "alms giving ceremony" is no more than the daily morning rounds of monks. Just roll out of bed at 05:00 and walk near any monastery on most any street and you can look for yourself without guide. For free.

Some of the excursions they have planned sound like you are going to be joined in with a bus load or boat load. So if that's not acceptable to you, I will say that you better make sure that if you expect a private tour for two people, that this is set up, contractually written, and priced that way. Not sure what legal/financial recourse you will have if your experience does not match your expectations, that is always more of a risk with tours than with own-arrangements. If you are working with a Thailand-based agent, most of them generally want to do as little work (i.e. customizing) for as much money as possible. And if you are working with a travel agent in your home country, most of them are just retailers and they are quite disconnected from the actual providers (not to mention few have extensive experience actually traveling in Thailand and being able to make sound value judgments).