FWIW, when I did my 3-week Vietnam trip years ago, I took a conventional north-south route and just did backpacker tours when there, as they were so cheap it was near-impossible to go lower independently. This included a 3 dayer to the Mekong Delta and 2 for the Ha Long Bay/Cat Ba. I would do the bus trips between cities otherwise, so after coming in from Cambodia overland (an adventure then) the bases were HCMC, Dalat, Nha Trang, Hoi An, Hue, and Hanoi. Great trip, even though I got pickpocketed (thankfully recovered wallet, just without cash). Average spend was $30 a day. I also saw some of the same people at every stop.

Have been to the Philippines many times...it's a place that gets a lot of sharply divided opinion but I would say needs to grow on you. It gets far less tourism than Thailand or Malaysia and there aren't as many opportunities to fly in and go see something right away. Boracay is the closest to a Phuket-like place and small and fragile. I've been to PPS and points nearby but not El Nido. Also Cebu. Bohol, Cagayan, Puerto Galera, Baguio, Banaue, etc. Banaue is definitely a "thing," and the Chocolate Hills in Bohol maybe a bit less so. Access takes some investment in time, though.

With Borneo I'd highly recommend a tour of the lower Kinabatangan (out of Sandakan, most likely) as it's really beautiful and very threatened. There were even orang-utan sightings on mine. The National Parks are also really beautiful. I haven't done the Mt. Kinabalu thing but I'm sure it's nice. KK lacks charm IMO but that may be because of being flattened in WWII (Kuching is better for that). Brunei is kinda unique.

Don't worry too much about the monsoons. At that time of year you might get a big but short-lived downpour around 5 p.m. or so.

Whatever you do, there won't be enough time and plenty of things on the wish list that'll have to be left for later trips. On my earlier trips to the region I really crammed the itins but also underestimated my ability to get back for more trips.