I've done two trips to Asia of about 5 months each with my partner, though we weren't solely in SE Asia, we ventured to other countries outside of that. The first trip was Malaysia - Myanmar - Thailand - Taiwan. The second trip was Malaysia - South Korea - Japan - Hong Kong / Macau - Thailand. We usually like to spend about a month in each country, sometimes a bit less, sometimes a bit more. We usually move around the country instead of sticking to one city so it's not super slow travel, though we did stay a whole month just in Bangkok recently.
Visa border run - never did it.
Seasons and festivals - yep, we take that into account.
Medical stuff - we get travel insurance. This covers for other things beyond just medical too.
Apartment renting - we usually go with guesthouses, Airbnb etc.
Motorbike or not - depends on the country, what licenses you have, your skill level. In many parts of SE Asia the laws are usually not very strict and it's not difficult for a foreigner to procure a motorbike without a license, and it can be very freeing and enjoyable to ride around the country. However these same countries often also have a high rate of traffic accidents. Assess the situation and risk level and come to your own conclusion.
Flights - we do some in advance, others not so much - I like to lock in cheap flights but also like to allow for some flexibility so it can range from as little as a couple weeks to as long as several months in advance. In our most recent trip, we decided to stay put in Bangkok longer than originally planned, so we forfeited a flight we booked (luckily it wasn't too expensive), and booked a new one. If you're doing an indefinite trip then I certainly wouldn't book all of them in advance. If it's a shorter one... maybe, if you have a reasonable idea how long you'd want to spend in each place, and find some great flight deals.
Other transport - whatever suits our needs. Bus, boat, taxi, train, horse cart, electric bike, etc.!