That's a tall order alright, and it sounds like - should all of that come true - there won't be much left that is a Paso. Although the Paso is completely enclosed like sportbikes, it's considered a sport-tour bike. Those 16" rims weren't meant for corner grip - they're built for stability at cruising speed. But onto your questions ...
re: the FI - I'd skip the 750 and go straight to the 907ie. Of the Paso line, it's generally accepted that the 907's provided the greatest power output from the get go.
re: dual headlights, I've seen a conversion done on a Paso with twin projector beams, and IMHO I thought it was pretty ugly. The only other twin round headlight bike I can think of is an F1 (same era as the Paso) that was fitted as an endurance bike:
re: paint - there weren't many blue Paso made in the first place; some consider them as limited as the white "Limited's". I have a blue '88 myself, and while I've been considering an alternate paint scheme - I've been keeping an eye on ebay for pieces and accruing them as I go. Once I get a full set, I'll paint it. Alternately, if I decide I can't wait, I'll order a whole set from Airtech-Streamlining (about $900). It's not the same quality as factory plastics, and will require some additional work in terms of getting it fitted properly (they aren't drilled for mounting holes) - but it'll keep the originals intact. Another reason for you to consider Airtech - the headlight cowl is not cut for a headlight - therefore you'd have a clean sheet to work with if you implemented twin headlights, however you decided to it - and you wouldn't have to worry about filling in the gap. In terms of value, there are fewer blue and white Limited Pasos than there are red. But on a personal note, as another blue owner, please don't paint it ...
Otherwise, Lucas, not to rain on your parade, but looking at everything you suggest from an objective, even fiscal point of view (which may not be an issue for you, I realize, but still) - you're talking about taking a motorcycle that is almost 20 years old, that was only available for a couple years and now only exists in limited quantites - and making into something else entirely. Which is completely in your power to do so ... but all these components that you're suggesting to upgrade or replace already exist in other motorcycles. Maybe they don't look like the Paso does, but if that's the only thing that attracts you to the Paso, it might be cheaper and less drama to retro-fit a set of Airtech Paso bodywork to a more appropriate chassis/engine. There would be less unknown to contend with; less problems finding parts or aftermarket options (which are few as it is).
Hopefully you don't take this a slam or in a poor way - it isn't meant that way at all - just trying to be objective about the ambitious project you have described here. Let me preface this next bit by saying that while I'm not an absolute "Paso Purist" - I do lean more towards maintaining the Paso's original intent than modifying it. (I have a '97 Monster, and that has been modified to be sure - but I think that was sort of the Monster's "original intent", too - modification!)
Anyway, everything you're talking about changing - I'm not sure what "Paso" would be left, besides bodywork. And on a 20yo motorcycle, it's my opinion that would be easier to ensure that your Paso does what it's supposed to, reliably - maybe add some refinement (either Jon Fiore's Weber tuning guide, or a Mikuni/Dell'Orto/Malossi/FCR conversion; Jon Slocum's electrical upgrades, etc), and that way you're cementing "that which is the Paso", versus trying to develop a modern day sport bike out of a 20yo sport-tour bike.