No , Don't Vacuum the Substrate!?

You want Just do a Water change! Don't disturb the Bacteria Colony anymore than you have at this point.
Maybe only even clean the front glass and not the others, only if you need to.
Beneficial Bacteria grows on ever surface in an aquatic environment. Including the Substrate. This is why whole water column movement is so important as the BB in the substrate and on every other surface will get slow and constant exposure during the regular cycling of the tank and prove to be really helpful.
The most efficient setup that someone could have would be a UGF system that has power heads facing down into the standpipes to push water down and under and then up through the substrate to move waste off of it and into the water column and then a mechanical filter. The Surface area of substrate for the BB colony is ridiculous! water would always be crystal clear.