There are many reasons for the pump spindle to fail. Among them (and the most common one BTW) is improper installation of the outer timing cover. If you have never had it off you can rule this out unless it is a used bike. Excessive runout of the crankshaft (.006" is the limit) but even that is a lot. Newer cranks only have .001 or less. Bad spindle - more likely in 1999 than now, Improper installion of the oil pumps, failed worm nut gear, bad fit of the actual spindle inside the timing cover (older bikes can be bad, but is highly variable). There are other reasons as well. Unfortunately and oil pump gauge really won't help much. The RE runs on a high volume, low pressure system and when they are hot the pressure can be less than 2lbs. and yet be perfectly fine. I would consider the following:
1. Measure the run-out of your crank. If you are getting it re-built your crank builder can do a lot to make this close to zero.
2. See how your new spindle fits into the timing cover ( is it a loose fit with room for the spindle to knock around?
3. Put in a new worm nut.
4. Inspect the teeth on your new spindle when you get it and make sure they are good. (rare but it can happen)
5. When you reassemble the timing cover and get the oil pumps installed you should be able to turn the spindle with your thumb. (maybe not easy).
6. Take a small drill bit and stick it into each of the oil passages in the timing cover. Then look using a flashlight see if it it meets the intersecting passage cleanly. (not at all uncommon in older timing covers).
7. Do your best to keep the engine from backfiring by making sure the timing is not advanced and the mixture is good.
8. When you re-install the timing cover put it on VERY carefully gently turning the crankover while you are slipping it into place by hand. This will prevent the threads from getting damaged as they engage with the worm nut.
9. make sure that you prime the oil filter cavity before you install the timing cover and use a lot of oil on both the spindle and the worm nut as you install them.