Were the Transport Modules based on the Technodrome Drill Elevators?
 

By Technodrome Drill Elevators, I mean the ones that were used in the 3rd episode of the old toon A Thing About Rats, the ones that got Shredder to the mansion. If the modules are standing up with the drill on top, they kinda look like those drill elevators so I'm wondering if the transport modules are from the same blueprints as the drill elevators.

I'd say so.

When they first use them in "Beneath These Streets" Krang says he modified something to make them... can't remember what though.

I believe it was that drill elevator that was modified, only to allow a free exit into the terrain as opposed to the surface. The modules were probably also modified again in Season 7 to form the amphibious modules.

Krang say's he modified the "Anti-Matter Cannons" to bore holes to the surface.