An Application Questions. Please advice

Hi All,
I have booked NCS for this month end. Please clarify on the following doubts.Some of them are answered quite some time back and with the pace HO changing forms and rules , answers becoming irrelevant so I have put the question again, Sorry about that.

1) For NCS - If anything missing or more docs required , will they charge money again ? or can book new appointment with them without charges ?
2) I have Laminated Degree certificate ? - is this any problem ?
3) My Old passport (with first entry seal) is missing , is there any alternative ?
4) Question 1 - I received my BRP during ILR taken Nov 2012 , Have a unique number on top of it , Can i write this a reference ? Or Caseid (give for ILR) ? OR it should be from Tier 1 reference or something ?
5) And I beleive Need to take another BRP for Naturalisation too .
6) I have PBS print out taken during Nov 2012 ,(most of the options selected during that tiem is nto available now) ,Can I use that ?

7) I have ONE Penalty during last 12 months as Stopping in YELLOW Boxed area , Charged by TFL (Tower Hamlets) , paid the penalty . dont remember its PCN or FPN , should I declare this ?
From Guide its states that
"You must give details of all criminal convictions both within and outside the United Kingdom. These include road traffic offences. Fixed penalty notices (such as speeding or parking tickets) must be disclosed, although will not normally be taken into account unless:
• you have failed to pay and there were criminal proceedings as a result; or
• you have received numerous fixed penalty notices."
8 ) Can I use my Accountant as Referee ? He is my Ltd companie's Accountant for last 5 years.
9) My wife did Bachelors in Travel and Tourism Management. This is not found in the PBS. But by selecting her university and selecting course as "Other" she is getting 10 points, is this OK ? Or does she needs to get NARIC certificate ? We do not have much time now ...
10) My Wife was part time employed for a charity Organisation and also she was part of a Limited Company on part time.Curently doing only Part time employment
So I beleive she should select "Employed" and should give details in Employment history with Ltd company details as well? She was Workpermit Dependant then T1 Dependant and ILR , So no work restrictions
Hope her multiple jobs wont effect her application ?
Kind Regards

Also if Last one year Employed(current) ,and before that Self employed do we still need to give "Self Assessment Statement of Account" ? Please some one clarify my doubts.

Could some one help clarifying my doubts please

I got my Old passport ,so ignore my 3rd question. But please do some one help on my doubts .

Kind regards