Going on about 30 years ago I spoke with Andy of Vintage Tubes (in Michigan) with basically this same question. I was interested in retubing (with NOS) a pair of ARC VTM 120s (6922s and 6550s) and a Cary SLP90 (12au7s). Andy's advice (which I followed) was to start "closest to you" which meant the preamp and then the signal tubes in the amp. The improvement in SQ was significant.
A few months later down the road I talked to Andy again about output tubes, and he wound up selling me a pair of quads of NOS Tungsols (not the Russian reissues that are out there now) to replace the Svetlanta 6550s I had in them. For as much money as I paid for those NOS Tungsol 6550s I was expecting a huge sonic dividend and I was disappointed. I really didn't hear any improvement. Maybe because I was expecting too much?
Anyway, going by that experience and Andy's advice, I would start replacing tubes from the front and work backwards. And I have heard good things about JJs for the price.