You really only have two options - unbolt everything and add a shim, or drill a hole in the top flange and pump in a setting compound.

Hi

Take a look at this site and check that your installation procedure follows this method.

https://acoem.us/blog/shaft-alignment/soft-foot-wh...

“Do not worry about your problems with mathematics, I assure you mine are far greater.” Albert Einstein

Is vibration analysis part of the acceptance testing of that machine?
Are some vibration limits specified?
Who is responsible if the installed vibration is excessive ?

Bases like that sometimes rely HEAVILY on grout filling to turn the base into a monolithic structure.
I think expecting cementitious or even epoxy grout to "stick" to underside of the top plate is wishful thinking.
The top plate by itself is structurally hardly more than a cookie sheet .
In my opinion There need to be several substantial engineered full width ribs welded to the underneath surface of the top plate strategically placed under the pedestal feet.
Some manufacturers offer bases with steel reinforcement adequate without grout as an extra cost option.

There need to be stiffeners/gussets in the base side flanges within a few inches of the anchor bolts.
https://i0.wp.com/theconstructor.org/wp-content/up...

Are those low rails at the far end of the skid provisions for mounting a drive motor ? They must have welded reinforcement in the nether regions as well.



And then there is the floor that the skid will be mounted on.

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