a) The Illustrative Valuation box is meant for information only. The real key is the Sources & Uses of Funds. The Illustrative Valuation should be a snapshot of the current valuation of the entire company (even if less than 100% purchase).
b) You can hard code the Equity Contribution as well as the Debt. Since you know your specific numbers and deal structure, then yes, definitely overwrite it (and make it blue). If you didn't already know it, the suggested deal terms read off from the BS page as you noted.
The Refinance switch comes into play only if you have existing debt, but you just mentioned that you don't have any debt, so this shouldn't be any issue?
c) After hard coding your Sources & Uses (effectively driving your Pro Forma Capital Strucutre), everything should flow through dynamically. The only issue might be if you have existing debt but you aren't taking that along. So an easy fix would be to have your Historical BS (last actual year have no debt on it - you'd have to find the balancer to make BS balance still).
d) This is commonly known as a waterfall (yours sounds like a simplified one, which is good). In the IRR page, add a new row or rows under EBITDA and do exactly what you just said. Keep the match as simple as possible. If you have EBITDA figures to achieve (vs growth rates) then hard code the EBITDA figures in a new row, and in another row, hard code the additional %ages to be received. These are both hard coded since its already been negotiated. Then if the EBITDA targets are hit, mgmt gets additional %age equity. This flows through to the Implied Financial Sponsor Equity Value (lowering it). and everything else updates. Create a new block of calculations for the mgmt's Implied Equity Value.
In either case, EBITDA should NOT change since this doesn't sound like a bonus paid in cash, but rather, additional equity. SO EBITDA shouldn't change and shouldn't be discounted, etc.