Install TRLE in a new directory and copy TR3Objects.h to that folder. Rename it to Objects.h to have the item names in TRLE.
Delete all original wad files and projects cause you don't need them. Also the sounds and music can be removed (or just not installed). Use a no-cd crack and place TR3 in the same folder.
Place TR3TombPC.dat in the data folder and rename it to TombPC.dat. This will enable level select.

Do the same for TR2 with TR2Objects.h and TR2TombPC.dat (so also a new installation in a new folder).