I did at trial run at pumping down the vacuum today.  While doing this I monitored the transmission power.  The graph of this is attached.

You can see the start, where therer is good transmission.  Then there's noise where I put the lids on the chambers, and then a locked section in the middle.  You can see that just putting the tops on the chambers and clamping them down has caused some misalignment.  Then there is noise where the pumping happens, and the last section is after the valve is closed and the pump turned off.  Clearly there is significant reduction in transmission power.

Maybe we can improve this with better clamps to hold down the vacuum chambers?  At least the cavity is still locking, so the overall effect is pretty small.

Also, I haven't tried to maximise the transmitted light by playing with the input mirrors.  This may improve things a bit.

No EPS, PS, TIFF, TARGA, GIF87, or BetaMax attachment formats allowed.