His income is PAYE. Pensions paid through the employer scheme are tax relieved on what is called the "net pay" arrangement so the Gross on his P60 and the tax paid on his P60 which both transfer to the Notice of Assessment will be after the pension relief. It will not show there.
Trade Union Subs, there's a box which must be ticked on the Tax Return (form 11) to claim under self or spouse. If that was not tcked, it will not show. That's even if it originally did show on his PAYE tax credit cert. The PAYE system and the self-assessment system have some walls between them and items like this don't automatically transfer.
On tax and the joint assessment, if his tax is in order then the tax left on the notice of assessment will be that from your self-employment. However, if there is any under or over payment on his PAYE then that will show as a plus or minus in the overall final result on the notice of assessment.