Hi Chris
There’s a few ways to skin the cat if you are willing to take the DIY route.
The “best” pickup arrangement is the rotor and pick ups off the fuel injected XJR. Pretty sure Randy (RPMracingca.com — the banner at the top!) can source those for you. This will allow you to control ignition as well as fuel. *** Don’t forget the XJR gasket for the pickup cover - it is thicker and helps keep the pickup from shorting out on the cover! ***
Another possibility is a “fuel only” install while using the stock (or even a Dyna) ignition. I think with this you actually use the coil (-) as the rpm source for the ECU. What do you lose by going this way? Maybe a lot less than you would first think. Without extensive dyno time with a very skilled tuner, you’re not likely to find much in the way of gains over the stock curves advanced a few degrees. If your going turbo or nitrous, then you NEED full ignition control.
Now to share a few lessons learned the HARD way:

1. You NEED a sump of some sort to ensure constant uninterrupted fuel supply to the fuel pump. Without one, anything less than maybe 2/3 of a tank of fuel and you can cavitate the pump. It will take you weeks to months to figure this out. And you’ll destroy a pump or two or three in the process. Carbs have float bowls which serve this purpose. If you don’t want to fit a sump, you’ll need to sort out an in-tank pump and baffle system.
2. I first used a Kawasaki trigger wheel modified to fit - also had to move the stock pickup far enough outboard to have to require notching the cover - fine for racing, not so great for all weather riding. Although the 24-1 arrangement “worked” - it started much quicker and more reliably after removing a second tooth for a 24-2 arrangement. The XJR fuel injection wheel is 24-2 - seems Yamaha understands the needs of these engines pretty well!
3. If you go with LSx coils - DO NOT over dwell them. They will discharge early to ensure the coils are not damaged from over heating - and will instead detonate and destroy a big valve race ported head and cams (exhaust cam specifically). There is still some old info on the net about what is a safe dwell setting - make sure to get the latest info! Don’t know if other commonly used coils suffer this issue or not.
4. Your wide band O2 sensor installation and integration is critical for tuning if you aren’t going to spend a LOT of time on the dyno (with a very knowledgeable tuner). Sensor grounds, proper power supply, and condition are critical to ensure the O2 sensor doesn’t take your reasonably well sorted tune and turn it into an unrideable wreck in short order.
Good luck!

The micro squirt is a very capable system I think it is better sorted than the Gen 3 mega squirt lineup — I think they have tried to do way too much and add way too many bells and whistles too quickly and all the functions don’t interact seamlessly - critical if you start pushing things hard!