Please call Women's Aid. They will be able to give you support. You should also find lots of helpful information on their website. I've not been through this personally but many posters have and some will be along in due course to share their personal experiences.
And please ignore what he keeps saying about taking the children away from you. As PP said - this is what abusive fathers say - he's trying to terrorise you into backing down. He knows he can hurt you most by threatening your access to the children. But he's lying and he will say whatever he thinks will scare you into backing down. And he will of course deny that he has abused you. In his eyes, he can do no wrong so don't expect him to admit to any wrongdoing. Don't expect him to help you with this process in any way.
Custody of the children is not up to him. There may be a few countries where the mother has no rights and the father calls all the shots but that is simply not the case in the UK (assuming you're here). The default position will be shared custody (not necessarily 50/50 but some variant of that) between the parents unless it can be shown that one parent poses a real threat to the health and safety of the children and serious evidence is required to show this. The courts take a great deal of persuading that a parent should not have any access to the children. Since you have been the primary carer, the children will almost certainly be based with you and go to him every other weekend and one night a week or something similar. Remember that since you have been primary carer, you have the advantage over him in any discussion as to how custody should be arranged.
Think about it logically - he's been prepared to let you do 90% of the childcare so how can he possibly say now that you're not fit to have the children? Similarly, you're a fully functioning adult - he can't just get you mentally assessed against your will and again there are no grounds: if he had been concerned about your sanity, he wouldn't have let you do 90% of the childcare. It's all bollocks, OP, designed to scare you into backing down so please, please ignore those threats. And please realise that you have rights, too. Not just him.
And as @crunchiebabe said: do consider whether you and the DC can safely remain in the house while this process is going on. Some parents manage to cohabit while separating but for others it's impossible. If he refuses to leave (and it's not easy to get someone out of the house against their will - the courts are unlikely to grant an occupation order without giving him the opportunity to contest it), then you may need to think about moving somewhere else. Is there somewhere you could go?