V1 is almost always the tube closest to the input, so you've got that correct. That is the tube that will have the most effect on your tone. Before going on a quest for new tubes, do two things.
Check all of your existing tubes for microphonics. Hook your amp up the way you will be using it, let it warm up and gently tap each tube with a pencil. It it rings, it could cause problems with your sound.
Use small pieces of masking tape carefully placed on an area of the tubes that does not have printing, the base is best if possible. Number them so you know exactly what position each tube is in now. Since there are two sets, maybe go A-1, A2, A3 and B-1, B-2 etc.
Then, re-arrange your tubes to put each tube in V1 position, listen carefully and take notes. If that makes a big difference, good or bad, that is something to consider addressing. If you have 2 great sounding tubes on one side and none on the other, consider putting the two best in V1 and moving the other tubes to accomodate that.
When buying tubes, the dealer is the essential link. Do they test microphonics? Do they have a return policy? Can you speak with them on the phone or via email and let them know what you are trying to accomplish? Those are all good things.
A friend of mine with over a dozen boutique tube guitar amps strongly recommends an eBay seller - eskimofridge - he's gotten excellent quality and service from him.
Output tubes and phase invertors (if the amp has them) are the next place to tube roll once V1 is chosen and the rest of the tubes are in good condition. Matched output tubes with a PI tube that has matched sections will sound "better".
Speakers make a huge difference in sound too, a perfect amp with the wrong speaker will sound worse than a not quite perfect amp with the perfect speaker.