Interconnects priority

In my experience the closer to the source the more important/impactful the interconnect can be.  If one interconnect is better/more resolving than the other then put that one on the source.  That’s how it works best in my system anyway.  Hope this helps. 

Or, looking it from another practical budget perspective, if I have a total of of $1,000 to spend is it clear that I should spend $500 on each XLR pair, or should I “overweight” my spend on one set because it’s the more “important” interconnect from a sound quality perspective.

I think what is clear in one person's system is not so clear in another. Here's another curveball- suppose the suggestion above is correct and the phono to the pre amp has more of an effect than the pre to the amp: would it be better to entirely "overweight" the spending by adding just a $1000 XLR from phono to pre, instead of 2 XLR's in both places?

I would lean towards the former, because eventually you will probably have the itch to upgrade the $500 XLR's, but if you have one $1000 XLR you would just need to upgrade one, and you would probably get a bigger "wow factor" by hearing what the $1000 XLR can do, compared to $500 ones. 

Providing of course you don't have a "throw away stock" XLR, and at least a Mogami or equivalent for the pre to amp XLR. 

My system only has one pair of interconnects.  I believe the simpler the system is, the better it sounds.

Jerry