Dave,
Using brackets in lieu of shims will work fine.If you limit the amount of attachments
may work better for you, corners and maybe ctr. posts only,let the rest float.Caution on vertical holes,they should be dead on.Remember each elevation change requires
a resurfacing process that should be minimal skimming.You could drill those holes accurately by drilling them after the fact using the Z axis to define elevation.The Z axis is the reference. The linear
guides are as I pictured also.If you mount them on separate adjustable risers, you will be able to tune them.Their needs are not just parallel but on plane as well.If you raise the table leaving the rails loose the trucks will show you where to tightened
the riser brackets.The explanation is oversimplified but in principle is correct,the alternative to this is less than exciting.I believe that somewhere you commented on
using c-channel on the table ,because it was easy to through bolt to.On my machine
I have +/- 300 drilled and tapped holes,in1/4 -3/8 walled rec tubing.The average
time to tap a hole about 90 seconds with a cordless drill--kind of a non issue.Unlike the rest of the world ,here in the US rectangular tubing is bountiful.Here's where you might want to do some more research.
Dave, the welding is for any part of the machine that does not need adjustment,Think about the jack hammer effect.Provided that you tie the moving
table to frame base 20mm is no problem.In other words don't rely only on the linear
rails as a form of attachment.

Anything taken away from the steel will retard performance.

This build is going to be very complex & demanding with no promises. There are too many alignment for a structure IMHO...
1) hole location,
2) linear slide line & plane alignment. & there are so many of them... we are looking at 0.05" to overload the slide...
worst of all, I can not find a reliable datumn to work from...

My original suggestion was for a scissor lift as prime mover, some rod in pipe guide as very primative guide to ensure the bed doesn't run freely & using locating pins to locate hole accurate enough & secure with bolt through to secure & strengthten.

For the locating holes, you don't want/need to drill in situ, drill a set of precision holes on a separate plate, then mount them on while you are alignming the bed.

IMHO, it will be near impossible to achieve your kind of objectives with fabricated steel structure w/o precision jigs which will cost as much as your whole steel consignment. & very difficult to carryout in your 7' headroom workshop.

The more I look at it, I am more inclined toward JLFin's suggestion of a removable sub base on a fixed bed. Since you have space limitation, why not a small fold away sub base which you can stow away under the bed.? eg, a few boxes at for handling by one person build to precise height. Looks really crued but guarantee to work.

I'm considering this with the overll picture that you are building this for your business use, hence, money & time are important.

I don't know much, but from experience of my many "shortcuts" over the years it's pretty difficult to lift something horizontally and then line up bolt holes. I've found that lifting at an incline and locating holes at one end, then doing the same at the other and locating the holes, the "filling in" between can be easier.

Not sure if you all came up with the ultimate solution already but I have a suggestion that is relatively low tech which might work. This may be what Ken was talking about above but anyway here goes...

How about creating one or more torsion box platforms out of light mdf. These would be the same dimension as your base support board and could be bolted directly to it to provide a raised platform. You could store them under the table when you want to work on thicker stuff.

There are plenty of places online showing how to make a torsion box and if you use the MM to make the ribs it would be very accurate. If you then surface it it should remain flat and true (in theory).

You could make thinner ones and stack them to give you some flexible height options.

Of course I could be way off the mark :)

Here is a sketch of what I mean (in xray view). I have left the ribs exposed around the perimeter to facilitate bolting and as a bonus you can use the lip to clamp work or a spoiler board...

...in the Theatrical world we call those stress skin platforms - and they work very well.
A good affordable solution for adjustable table height.

Sean