The 500cc V4 is notorious for the carbs clogging after it's been sitting. There are a LOT of tiny passages in there, and the carbs need to be immaculate on the inside, or you'll run into hesitation, strange running, and performance issues.
First thing you should always do when you're not sure if it's fuel or spark is shoot some ether (starting fluid) down the carb throats and try to start it. If it catches and starts running, you know you've got decent spark - decent enough to run at least. Saves a lot of headache diagnosing things.
Also, very VERY few motorcycles actually use CDI ignition. (Capacitor-Discharge Ignition). The V4s are TCI - Transistor Controlled Ignition. Basically you have two identical spark boxes on the 500V4. One of them drives the electronic tach. If you have running issues where it feels like two cylinders drop out, check your tachometer. While the bike is running (poorly) does the tach read zero rpm, or alternatively bounce around crazily? If not, swap the spark boxes. Does it do so now? If it does, you've got a bad spark box. (Check the harness, the connector with the extra wire is the one that drives the tach, and now you know which spark box is bad).
I had the VF500C, which is the cruiser version with the same engine. I'm not sure about the F, but the C did not have a rev limiter box. The bigger V4s have two boxes, one with a white connector and one with a red connector. The red connector box has a rev-limiter built in (cuts two cylinders at 12k rpm). They are interchangeable, and you can run the bike with 2 red or 2 white boxes. With 2 white, you won't have a rev-limiter. With 2 red, all 4 cylinders cut out at 12k. Note that the bigger V4s have a 10k redline.
Boxes from different 1st gen V4 bikes will swap in and out without issues. HOWEVER, the advance curve may be slightly different between boxes. You can still do it, but in that case you should replace them in pairs. I didn't notice any performance issues running my V65 Magna (VF1100C) with V30 (VF500C) spark boxes, and I keep a pair as emergency spares in case of a failure on the road. Also, since the larger bikes have a lower redline, you may want to avoid the boxes with red connectors, as they'll cut out sooner. Then again, maybe not:
The 500 V4s have fragile wrist pins. Don't spin them past redline. My first bike was a V30 I got in boxes, because of that issue. Broken wrist pin, scored cylinder wall, but fortunately it broke at idle and the PO shut it down immediately, so a honing fixed it enough to be a runner again. (It burned a little oil, but I could live with that).
Also, dunno if it makes a difference but the V30 Magna and V30 Interceptor (VF500F) have the exact same motor... but the Magna has 500rpm lower redline. 11,500 on the magna, 12,000 on the Interceptor. There is no difference to engine internals, the only difference is printed on the tach itself. Just keep away from redline if you want your motor to live!
Charles.