Phillip - On your own? From the UK. I would go to lumbalumbadiving.com. You won't feel on your own. Dutch run - they speak English better than I do. There have been previous posts here from solo travellers who have enjoyed the welcome there. They'll pick you up from the airport - no problem. Totally professional outfit, excellent guides who have worked for them for years. They'll organise transfer to Lembeh in liaison with your chosen resort and if you want to take a bit of time out and go up the volcano or tour the highland area inland - they can do all that too.
Roel keeps an eye on special offers on flights out from Europe and may be able to give some advice. Although long-haul, it is very straight-forward with Singapore Airlines to Singapore and SilkAir (their "sister") out to Manado. Possibility of stop-over in Singapore. There are also possible routes via Kuala Lumpur.
If the missus likes to lounge and read - she could stay in the beautiful cottages with the verandah and views and get a massage in Juud's spa room or she could come out on the boat and sunbathe on the roof, sleep in the cabin and snorkel, have lunch with you before your afternoon dive. lumbalumba seem to be popular with non-diving other-halves because it is friendly and relaxing. Food is excellent.
Cottages have hot water, fans and air-con (back up generator so this all works!), showers big enough for two, large beds - err hem . . . Oh well, if you're on your own you will just have to run around the cottage to make use of the space!
You will enjoy North Sulawesi.