Hi SV
I'm concerned when you write that RF might come back over the power supply bus. This indicates that you are not confident that your power supply line filtering is adequate. Did you use coaxial feedthrough capacitors on all power supply and control wires going into the LNA box? You should. These capacitors are the optimum way to guarantee good shielding. If you use these, with a suitable value of capacitance (like maybe 1000 pF or 10,000 pF), then you will have insignificant RF getting through on those lines.
Years ago a friend of mine built his "ultimate HF receiver". He was an expert RF engineer. He built in the modular fashion, with major sections each in their own box, as you might be doing. He built each section using double sided pcb stock, and all components were mounted up in the air on insulated low capacitance standoffs that in turn were soldered to the ground plane of the main pcb. The boxes were sealed shut by soldering more blank pcb stock into a box around the main board, using the main board as the bottom of the box. He ran everything into and out of the boxes through either coax connectors or feedthrough capacitors mounted in a wall of each box. This method of construction gave the best isolation performance that I have ever seen. Admittedly, it would be a pain to repair inside a box because you have to unsolder the lid, but otherwise they were great.
If you are building the ultimate, you should aim for excellent shielding performance in the same way.
As for mystery mixer outputs, I presume that you are familiar with using nomographs to predict mixer products. I've seen what you describe and it can be quite mysterious wondering where all those mixer products are coming from. On the other hand, I see the fewest from double balanced diode mixers and the worst from home made single transistor active mixers of various kinds. In any case, reduction of products comes from your choice of IF and LO frequencies as well as the performance of the mixer itself. Also be aware of 2nd order products coming from your LNA or from your LO.
DO you have a preselector on your LO?