I'm inclined to put my two working original tubes in V1 and V2 and leave the JJ in the phase splitter slot.
First thing to know is that a 12AX7 (well, 12A<whatever>7) are dual triodes, that is 2 triodes (2 gain stages) in one bottle, so you really have V1A, V1B, V2A and V2B (and eventually V3A if the amp uses a cathodyne PI).
Usually V1A (first triode of V1) is the very first gain stage, which has the more influence on your overall tone and is the most subject to microphonics issues - obviously since everything else will amplify what this stage produces. What V1B and V2 are used for really depends on the amp, and V3 is most often the PI (if a long tail pair is used) or a last gain stage + a cathodine PI (typically the Peaveay Classic 30).
Now I don't have the Roadhouse schematics at hand and google was not my friend, but unless it has a tube-buffered loop, chances are that the boost part comes from either V2A or V2B but it might come from V1B too, cannot tell :-/
Anyway: odds are that your microphonic preamp tube was V1, so putting it back might not be a solution - but that's easy to check out. You could also try your old V2 in V1. Or even swap your new tubes positions and see if it makes a difference, which would not be such a surprise given the very wide tolerance wrt/ specs on current tubes.
Ok, not really an helpful anwser, but without the schematics it's really a wild guess game :?