Is there any way to overcome the dissy problem? and what exactly is a cut and splice job?
First - this is a topic that has been beaten to death on the internet - start searching, the answers are out there.
Personally I have not put a GTi engine into a Samurai, so I can tell you what works and what doesn't - I am on the other hand quite familiar with the different versions of the 1298cc G13B engine, so I do know that the crank can swap (I've done it), and that the transmission will bolt right up without an adapter plate (the Swift & Samurai engines use the same block).
I've heard of people beating a dent - sorry reshaping the firewall to clear the distributor, and using a Mazda (I think) distributor cap, right angled drives exist or you could switch to a direct fire distributor less ignition.
You've never heard the term "cut & splice"? It refers to the work required to modify the wiring harness(es) to make them work. The original Samurai wiring will have all the connectors for the lights etc., but none of the connectors for the electronic fuel injection system - so you (or someone else) has to disassemble the two harnesses, and make them one - removing wires that aren't necessary, cutting wirings that are too long, extending wires (by splicing in another section) that are too short . If you're not familiar with the wiring of the vehicle before you start, you will be - very - familiar with it by the time you're done, and no it's not difficult, but it is also not for the inexperienced.