I'm a bit confused here, how did you have the matrix repaired? The matrix is obviously in the heater box and this is positioned behind the facia, two pipes extend from the box into the engine bay through the bulkhead where they are connected to rubber tubes a,s part of the coolant system. To repair the matrix you must have had to remove the facia.
You are right that water loss from the matrix will flood the footwells as I know from experience! The carpets are individual for each of driver and passenger, ie they don't lie over the transmission tunnel and therefore you don't need to remove the centre console (though it may be worth slackening off the screws on the console to allow easier prising of the carpets out. You will need to remove the cill panels (carefully) they are attached to the car via fir tree connectors and just pull out. Similiarly on the nr side you will need to remove the fuse box cover and maybe slackent the box itself. The carpets will just lift out now.
Now do a good clean, sweep, wash of the footwells, here is the potential for project creep, as you have the outriggers exposed take the opportunity to inspect for rust and treat as necessary (there is an excellent thread, search 'what to do about rust on the outriggers'').
It's all a part of the joys of motoring (particularly Elan ownership), good luck

You know more than you think you know, just as you know less than you want to know. ... Oscar Wilde