How to score pulse amplitude spectrum of special particle such as proton, triton, alpha?

That’s right, because the particle identity check should be done with JTRACK:
* alpha
IF (TITDET(JSCRNG).EQ.'detect1 ') THEN
IF(JTRACK.NE.-6) LSCZER = .TRUE.
* triton
ELSE IF(TITDET(JSCRNG).EQ.'detect2 ') THEN
IF(JTRACK.NE.-4) LSCZER = .TRUE.
END IF
being IJ always equal to 208 for an ENERGY deposition event.

Also, you may want to lower the 4-HELIUM and TRITON transport thresholds by means of PART-THR (1 keV kinetic energy - per nucleon - is the hard limit).