I haven't done the exact math, but if you are saying that 25% federal income tax was withheld from the severance, you are going to be close to paid in without doing more. Try running the numbers like this:
Let's call the bonus $166,667 (assuming 40% tax came out), plus $46,300 for 5 months, plus your $40K from the S-Corp. I will assume that depreciation reduces rental income to a negligible amount. That's $252,667 gross.
I can't tell how much went to the 401k, let's call it $5,000. Now we are at $247,667.
Even if you don't itemize, the standard deduction is $12,700 and personal exemptions are $8,100. Now you are at $226,867 taxable income. That's without itemized deductions and no deductions for your S-Corp. The tax on that based on the brackets is about $50,407.
If you withheld 25% on the severance, that's $41,666 paid in. If you withheld 25% on the $46,000 of salary, that's another $11,500, if you withheld 10% on your $12,000 salary, that's $1,200.
All of that is $54,367 paid in. You'd be due a refund.