1) The stock engine control management system (P12 ECM) does not accommodate an ethanol sensor, so if you go from 93 octane gas to e85, you would need to change the tune. I plan to do this with HP Tuners, but will need to bring my laptop and HP Tuners tools with me to a gas station to be able to change tunes.
Another option is to switch out the P12 ECM to a more modern one. The E67 could be used on the LSJ, if you are willing to do a fair bit of work. Read up
here and
here. Of course you could always drop $1000 or so to go to a stand alone system like Holley or Haltech.
2) I think the LSJ fuel pump is good to about 400 hp, and can pump ethanol.
3) Yes you could. A boost reference fuel system would be a nice upgrade for the LSJ, as it allows big injectors to have more range. Big injectors often have issues at idle, as it is hard for them to dispense small amounts of fuel.
4) Well, if it was me, I would do it later, but then I have pulled my engine for the last 2 winters doing upgrading. I wanted to get to know my LSJ health before upgrading it. Now I know that the bright green 32lb/hr injectors are at 100% duty cycle when I drive the engine hard. I know my fuel pump puts out 60+ PSI pressure when driven hard. I have replaced the broken manifold air pressure (MAP) sensor, the worn out intercooler pump brushes, the broken bolt holding the cam chain, and the faulty cam chain tensioner. All good maintenance items before adding performance upgrades.