Ubud is under 1000ft so it's fine if you want to go there from Tulamben. It's going to places like Bedugul, Kintamani etc where you'll get altitudes upwards of 1500-5000ft.
I'd do Ubud and whatever sightseeing at the end of the trip and do the diving before the trip. That way, you can test the housing and have a few days should your bags go missing, buy stuff you need on the trip etc. What better way to break jet lag than to eat, dive and sleep. Also any souvenir shopping can be handled without having to leave it at some office somewhere etc.
I recommend you take a guided walk around the padi fields in Ubud, especially when the light good (7-9am, 4-7 depending on when you go). If you want to splurge on nice accommodations, this is the place to do it, especially if you go to places off the main town center of Ubud. There are 2 very decent restos in the town center, Lamak (nice decor and food is good) and Nomads (good for tapas but a bit touristy). My fave restos are Mozaic, Cascades and Kemiri. You'll need reservations on weekends or daily if high season.
I'll reiterate my recommendation to dive the wreck and most of the sites south of it from a boat. This is much easier with a camera and you can finish up on the section of the wreck you want to concentrate on or wherever without having to swim back to the rocky shore (especially important when the waves get a bit big!). You also drop right next to the school of jacks and shoot them vs having to swim out to them only to find they've moved. With the dropoff, you can dive it no matter which way the current is going with a boat, whereas you are limited in direction from shore. If you get bored of the wreck on a crowded day, you can swing up to the coral gardens or other sites adjacent to the wreck and the boat picks you up wherever you end up. At the resorts with boats, the crew will unload everything for you if you want. I tend to carry my own photo rig as I think it's unfair to put ask other people who can't ever afford to pay for any damage to be responsible for my rig. But that's just me.
IMHO, the Mimpi Tulamben is not an alternative to the other places I've stayed at in Tulamben. The place is getting old and only the ocean view cottages are nice (except for the price they are not worth it). The restaurant is unimpressive (but then again Tulamben in general isn't a place for haute cuisine
).
Outside of Southern California, Penida is one of the few places where molas are seen regularly, so if you haven't seen one before, I'd make an effort to try. Plus the ones in CA are different from the Indo ones anyways.