Aligning Gearbox to engine

[Kimdeg123]

Hello,
I have recently just changed the clutch in my 1994 Suzuki samurai 1.3. I have done this before with no issues. Today, I took out the gearbox and engine as one (due to other project work going on for ease) and installed the new clutch and thrust release bearing and now cannot get the gear box and engine close to fully come together. I believe the gear box shaft is going through the spline in the pressure plate but this still leaves a good half an inch gap remaining in the bell housing.
For info: used a clutch alignment tool & have checked it twice before asking for help.
Any advice would be greatly appreciated, or has anyone had this issue before. Would be great to get the old girl back together.
Thanks in advance,
Kim

[ScottieJ]

Is there any chance you accidentally fitted the clutch disc in backwards?
Also worth pulling the disc off and checking the splines are sliding freely onto the gearbox input shaft.

Is the release bearing fully seated on the input of the gearbox?