If the noise comes out of the speaker on every channel, it could be a power tube or V1. If its just the 2nd channel, it would be the power tubes, V1, or V2. If its the 3rd, it could V1, V2, or V3 and the power tubes. I don't think the phase inverter would cause an audible problem as you have described, or V5 for that matter... As far as swapping tubes with the power on... i believe.... (check the manual because I think I remember reading it there) that you can pull one power tube at a time while in stand by, if only for a very short period of time. Same what surfcaster said. But check the manual. I don't know if this rule covers pre-amp tubes. When trouble shooting keep this in mind. Power tubes and the phase inverter (V4) will affect all channels. V1, V2, V3 pre-amps correspond to each Ch 1, 2, 3... BUT: Channel 3 uses V1, V2, V3 (cascading gain stages) and Channel 2 uses V1, V2... and so on.
My overall suggestion would be that if you are taking this amp back to the store, don't spend your own money on tubes. Suggest to the store that if they plan on trying to sell this item, they are probably gonna have to retube it, and maybe they should just supply a whole new set for you for now so you can use it. You are their customer, and you are spending a good chunk of money. Its not like this is a $100 practice amp...