So I've read that small modifications to the tune are free, if I get the tune and then mpfab's turbo to cat-back exhaust with no cats will I need to pay the $100 or is that considered a small mod
You are correct that minor tune adjustments are free. Large mods, that drastically change the operating behavior require a $100 retune.
Examples of mods that require a major retune ($$$) would be larger injectors, porting the intake manifold, turbo swap, cams, etc.
Almost all bolt on parts do not require a major retune, so they are free. Intakes, intercooler swaps, BOV, and exhaust are minor adjustments.
For example if you get the tune AND then get a turbo back exhaust you would only need to datalog the car after adding the exhaust, send in the log for analysis, and either get a free revision OR very likely receive an "all's good" response. Even thou exhaust work yields more power they usually don't require any ECM tweaking.
You will also need to disable the catalyst monitor using EZFlash to keep the CEL from popping up.
There's 2 ways to switch between E-85 to gas and vice versa (after getting the 42# injectors).
1. Is to run the car really low on fuel, refill with the desired fuel and reflash the correct tune (gas tune for gas, E-85 tune for E-85). If you go this route request both fuel tunes so you have them when need be.
2. Install a fuel composition sensor from a buick regal and wire it to the ECM. TriVince can then enable the flex fuel tables and you can safely run any mix of fuel and ethanol without any additional work.
Swordsmith did a nice DIY install that's somewhere on the forum, I recommend finding it as It's very informative.