Does anybody have actual temp comparisons between the old Xenon "heatpipe" cooler and the new aluminum one? I'm about to perform a reflow and would like to know if I should use the one I have or swap it with my heatpipe one.

Don't have extremely accurate temp measure for heatsinks but I always use the gen2 none heat pipe heatsinks. For the GPU I use the 1st gen non heatpipe unless i am installing a intake fan over the extra heatsink.
I have reflowed a few systems for personal use and for friends and have had no issues. I don't think which GPU you use really matters but I would go with the gen 2 CPU heatsink.

I was just wondering, because you'd think the heatsink with the heat pipe with thinner fins would transfer heat to air better. I think they switched to the non-heatpipe CPU cooler because of the budget.

From what i have seen, it's recommended to keep the copper heatsink on any xbox with a 90CPU.