1) Is it £993 plus the £600 NHS? I never got a biometric card, so I'm assuming I'll have to pay the £56 for that and the £19.20 for fingerprints.
No, the biometrics card is your visa, so there's nothing extra to pay for that (it's part of the visa fee). However, you will have to pay the £19.20 to give biometrics.
So, you pay:
£993 for the visa application and BRP card
£500 IHS surcharge (not £600)
£19.20 biometrics fee
Total = £1512.20
HOWEVER, the visa fees usually rise in early April every year, so I would get your application in before that happens, otherwise it could potentially cost hundreds more.
2) I can't apply until 28 days before the visa expires, but it takes them 8 weeks to respond. Will my right to work expire if they take too long, or am I covered because my application is processing?
If your visa expires while the application is processing, your immigration status is simply extended until the decision is made - so you can continue to work. So, as long as you apply before April 9th, you will be fine.
However, if you have a spousal visa, it is valid for 33 months, but you can apply up to 28 days before you reach 30 months... which may be up to 4 months before you visa expires, depending on when you entered the UK.
From your previous posts, it looks like you entered the UK at the beginning of August 2015?
In which case you can apply for FLR(M) any time from early January 2018 (28 days before the date in February that marks 30 months) up until April 9th 2018.
3) Have you had any trouble with the online system? I think I want to do that as it is pretty straightforward looking, and then post my documents.
I would NOT recommend using the online application. It's confusing, the questions are different and ambiguous, the application process is different and the visa is processed in a completely different city to the paper forms. Also, we can't see the online form so we can't help you fill it out.
I would definitely use the paper form to apply:
https://www.gov.uk/government/publications/apply-to-extend-stay-in-the-uk-as-a-partner-or-dependent-child-form-flrm