He'll take a bit of time to get over that deep clean - which was necessary but unfortunate, but I'm sure he'll bounce back. What can help them get over it is a bit of distraction. Eg scattering some food as well as just putting it in the food bowl. They like foraging for it and it helps them start using the cage again. Also keep talking to him gently. Hide a couple of special treats each day in different parts of the cage - eg one in his wheel, one somewhere else in the cage. It'll again help him want to use the cage and distract him from the upheaval and changes. Eg a tiny bit of cheese (smelly - he'll find it). Or his bit of daily veg in the wheel instead of the food bowl.
What cage is he in at the moment? A good option for a dwarf hamster is the hamster heaven - but without all the colourful plastic stuff (most of which isn't suitable for dwarf hamsters). But it has a nice big front opening door and that helps with taming and interaction - and less nerve wracking for them than having things coming from the top.
It's not a cheap cage but sold in a number of different places (pets at home, Amazon, Zooplus) - and you can also find second hand ones on Gumtree and ebay to save money.
It seems a shame to not use all the colourful plastic shelves, tubes and penthouse but they really do more harm than good and are just throwaway things to sell the cage! Starting with an empty cage and the tubes blocked off with blockers is the best way - and keeping existing items and adding a few more (cardboard is your friend - you can make houses, floor tunnels etc).
Zooplus is probably the cheapest place and they give you a choice of couriers to use at Checkout.
Hamster Cages | Buy the ideal cage for your hamster at zooplus
I worried myself stupid over every little thing when we had our first hamster. But don't worry - you'll start to bond over time and things will get easier. I made some big mistakes at first. Moved him cold turkey from an awful little plastic cage into a bigger one and it really stressed him. I felt so guilty. And realised in that moment that he wasn't just an item to be moved but a little thing that need nurturing and was dependent on me to be more careful and considerate. And I think at that moment I fell head over heels in love with him!