MN1 + SPOUSE VISA?

Hi there
I am British by descent with 28 years of evidence of living in UK.
I currently live in Malaysia with my Malaysian husband and children.
I want to get them British citizenship partly for their future but partly because I need to return home urgently to live there, because my father is sick and I need to care for him.

I have spent 1 year compiling all the information for the MN1 application form.
My children are 2.5 years old and 3 months old (yes... I started before the second one was even born!)
Now I have sent this off but am finding this is taking forever, and the biometrics etc is impossible (there are no appointments at all!).

My original plan was to wait until they received a yes or no on the MN1 and then proceed with my husband's spouse visa - my logic being that if they get a no, then I can get them dependent visas on his spouse visa... however it is taking such a long time that I now fear it will take at least another year before their MN1 form is approved, and so I think I need to apply for his spouse visa now...

my question for you is... can I apply for his spouse visa now? and then if their MN1 form is declined, apply for their dependent visas on his spouse visa separately later? or do they need to be applied for together?

my other question is - Is it possible to spend the three months of a holiday visa in the uk, then leave and come back a few days later like a visa run? because that may be my only option to bring my children with me, and look after my father

I have spent so much money and time trying to organise this and my head is drowning and so is my bank account. We have the required savings for the spouse visa, but not a penny more.

please help