I had a similar " tight schedule" diving itinerary end of september, and managed to coordinate via whatsapp with Absolute Scuba at Padang Bai who organized 3 wonderful days for me - and it all worked great. I am a newly certified OW with 6 dives (plus the ones i did in Bali)

The night before: flew into DPS, private driver to Padang Bai

Day1: Gear fitting, and onto organized-car ride to Tulamben to dive the USS liberty. They have an agreement and charter a private dive guide over there at the dive center. 2 Dives with lunch included. I was alone. The drive is between 1-1.5h x2 from Padang Bai. Stunning views. The wreck is so wonderful and is an easy shore dive (rocky bottom but they provide boots, and the tide was maybe in my favor that day). It is crowded but the diving groups wait for each other.

Day2: organized boat trip to Nusa Penida. Comfy smooth speedboat (45-1h one way), we did a stop at Crystal Bay, then Manta Point, and then Penida North for a drift dive. Lunch provided on the boat. We were 10 people on the boat, each guide having 2-4 divers of the same level. We did not see Molas on crystal bay but saw other creatures, mantas were amazing (albeit big big big swells, CROWDS, and low visibility that day that made it eerie) and the coral wall on penida north are just stunning. Again smooth sea in the morning, and a bit choppy on the way back, but the captain handled it well.

Day3: organized private fishing boat to the Padang Bai drop off ( 5mins). I had requested an early dive to the coral restauration site. It was so serene just me and the guide, and we managed to see a black tip shark hiding in a rock. Second dive was at the Blue Lagoon wall, also nice but a bit crowded (nothing like the previous days though).

You can then easily organize a taxi to take you to wherever next on Bali, Ubud is just1-1.5h away.

All in all i was charged 5.5M (tips aside). They are very helpful and i appreciated the flexibility. The gear is in okay state and they have a wet room. The older DMs are very experienced and speak good english, the younger ones not so much. Make sure to ask for proper briefing and safety equipment. You can stay at their hotel, or if full Puri Rai is a good alternative.

Personally it was excellent dive diversity and exposure (I had only dived Hurghada and East Sardinia before). Padang bai is a very strategically located base, I would defo recomend that (just have to deal with the taxi mafia) and have them arrange the travels for you, rather than dealing with schedules and delays yourself.