First of all.. you already did a lot of thinking before even starting.. that's good
pity you lost your job, but then , you already got a new... so who still cares about a company that can't even afford employees..
Those strips you mentioned are "linear encoders" on a manual machine they show the position on a Digital ReadOut (DRO), on a CNC, they tell the Control where the axes are.. ( and show you the positions on the screen )
looking at the dimensions (and calculating them to Metric .. yup.. i'm a metric dude 1.22m x 0.61m ) we're looking on a relatively big machine... so your choice for a Gantry style machine is also my choice...
if you want to "upgrade"to an ATC later on, i'd make on axis slightly longer to mount the ATC rack with tools behind the table ( or beside it, depending on desired size )
a nice solution for driving the axis along the table is, one ballscrew on each side, with a stepper, or servo motor on each spindle ( and a Toothed belt connecting the two spindles on the opposite side, so they will allways run equal..
if you make your gantry wide enough, you can mount the milling head between the rails.
if you want a real ridgid machine, i'd use two rails above eachother along the table on each side ( it's gonna cost you some this way) or, build two "ribs" on top of which the gantry-bridge will run, so you don't get that much momentum in the gantry as such ( furthermore, the rails and spindles will be sitting high ( and dry ) above the table, in case you want to machine with coolant ( if you mean stainless steel Aisi 304 with "304 ss") those high ribs will also make great "spatter screens" to prevent your workshop from getting all messy..
looks like a great project.. show us some drawings as well....