For example, one big issue I'm facing is how to handle the legal and tax issue of continuously depositing more and more cash into a business as it comes in from another income stream. This becomes really complicated not just from the perspective of how this affects other equity holders, but also the question of deducting the loss from my income while the company is not yet profitable.
LLCs and S-Corps are touched upon in the handbook but the issues around stock basis seems to really complicate the situation fast without providing much benefit for the deduction part.
I would think this would be a common issue since many founders aren't going to raise money beyond angel/f&f initially and will need to self-fund until they do or until they break even but I have yet to find good compliance resources for bootstrapping.