Turn the fuel petcock off and unscrew that 17mm nut off the bottom of the carb. Make sure your main jet is still screwed in.. Just saying, it happened before!
1000ft is nothing, really.. Something is amiss. First thing I'd do is try the needle in in #2 and #4 positions. But in the mean time check carb boot connections, reed block is nice and tight. Basics.
●Rereading your post i noticed you thought it was lean
If you are quite sure its too lean go richer on clip/main to confirm
Cold starting is your pilot jet,ignore for now,it will have no effect on your topend.
If the topend feels smooth flat its prob lean,if its burbly flat its prob rich.very hard to tell from a flyby vid.if in doubt go rich on main/clip first,its safer and will confirm which direction to take.
Bigger jet no is richer,clip 1 (top of needle)is leanest,clip 5 is richest
You won't jet around a mechanical condition.. so besides the info you've been given I have a few questions.
When you rebuilt it did you put the same base gasket stack in? Where was the piston in relation to the floor of the exhaust port? Did the piston arrow point towards the exhaust? Ring ends gapped?
What was the squish clearance? If you've changed the base stack and increased compression and decreased squish you can end up tuning the bike to favour low to mid and the top end while revving through won't be producing an impressive peak HP. The curve can be tuned, and by nature a 300 isn't going to feel as peaky as a 250.
Did you remember to put the o-ring on the rhs of the crank case, behind the bushing that the pri seal rides on? Could be pulling some gear oil at higher rpm.
As others have said, rich will stop revving in that it will break up and burble.. lean will make noise but won't pull and fall flat.
The reason I don't think it's mechanical is because it was running really nice for approx 15minutes before powervalve issue then after I had the plate welded it ran really nice again, I had a good 10 minute run on road where I used every gear 1-6 and all in the powerband too and it ran perfect.
So it should simply be a matter of determining what has changed between then and now.
The in and out play on the PV drum is somewhat normal. I doubt that is causing your issues unless if it's binding something up as it opens, but you said you ran the engine with the PV cover off and watched it open with rpm.
Have you had the PV flapper/drums out again while having it rewelded. Double checked it's assembled correctly? Didn't leave anything stuffed in an exhaust port/pipe while it was off the bike?
Do you run an inline filter between the tank and carb? Double check your main jet. It doesn't take much to block it up (or severely restrict its flow).
What's the spark plug tell you? This is one of the times you could do a pull chop at WOT and see if the engine is over/under fuelling. A new plug gapped and installed wouldn't hurt either. Particularly if it's been changed between when it ran strong and now doesn't.
This girls playing hard to get on ya for sure! Hang in there mate!