As far as I know, they usually don't communicate with us in the middle of the process even if we take the initative to ask them. I actually submitted an additional job description letter around 10 days after my eAOR via webform, and they then forwarded it to my VO. I didn't ask them if they needed it. I just sent it.
As to the proof of fund, I do feel their criteria are opague and there may be some unwrittern rules about it. For instance, they may consider the liquidity of stock as not enough for the fund to be "readily available", so we don't really know which degree of liquidity is required. Also, they may feel that stock is a high risk asset that may lose its value if the stock market indext declines.
Do you have easy access to an immigration consultant? I think you may need some professional advice on this. My personal understanding is that in order to appeal, your initial document should be able to withstand a second assessment by a senior officer during the appeal process, instead of using newly submitted documents to prove they shouldnt have refused your application in the first place. If your arguement is based on those new documents, then they can say you need to apply once again rather than ask for the initial application to be reopened.