While I'm sure what you have written makes sense to you, I found some of the detail a bit confusing, however:
Re: Q1.: (CAT is not my area but my understanding is...) The inland revenue affidavit was submitted in order to get grant of probate, and had the original cowboy valuation on it. The IT38 is filed when the disposition has taken place, so was based on the lower, more accurate, valuation. Revenue want to know why the discrepancy. The solicitor should be able to manage this one.
Re: Q2.: Financial institutions are required to give Revenue certain details in relation to deposit accounts and interest earned. They want to know what was the source of any monies you had on deposit in / since 2008, to ensure that they weren't from an untaxed source. Coupled with Q1 it would appear they believe there may have been some kind of messing around with money in the family, or that you received some cash, without gift/inheritance tax being declared. Assuming everything is legitimate and above board you should have no problem clarifying things to their satisfaction. In this regard, an interest cert is NOT what they are looking for, or certainly not all that they are looking for; they want to know where the money that earned the interest came from... i.e. was it saved up over time out of regular PAYE etc.. earnings (bank statements would prove this).