If I animate jace, cunning castaway and I put a counter on it with experiment kraj and I use jaces ultimate with kraj will it still make copies of jace provided he is still on the battlefield to be copied
When you activate the "-5" ability Experiment Kraj gains this way and then it resolves, you create two tokens that are copies of Experiment Kraj (not of Jace), except they're not legendary. Where that ability says "Jace, Cunning Castaway", read it as "Experiment Kraj" (C.R. 201.4b, 201.4). Note also that even though Experiment Kraj isn't normally a planeswalker, in general, only one loyalty ability of that permanent can be activated each turn, and then only once that turn (C.R. 606.3).
Is there a specific reason for it, or is it simply that it refers to itself using a specific card name to simply it?
Right, by default cards refer to themselves when their names appear in the text box. Cards that take other cards' abilities effectively overwrite the other names with their own. The exception is when they refer to cards/permanents "named" a name, in which case it cares about a specific card name.
201.4b If an ability of an object refers to that object by name, and an object with a different name gains that ability, each instance of the first name in the gained ability that refers to the first object by name should be treated as the second name.
Example: Quicksilver Elemental says, in part, “{U}: Quicksilver Elemental gains all activated abilities of target creature until end of turn.” If it gains an ability that says “{G}: Regenerate Cudgel Troll,” activating that ability will regenerate Quicksilver Elemental, not the Cudgel Troll it gained the ability from.
BWTeysa, Orzhov Scion Combo
GUEzuri, Claw of progress Morph
GUBSidisi, Brood tyrant
RWGisela, Blade of Goldnight Random red white cards i dont use.dec
GBLoam Pox
Modern
UBFaeries
GBWGoyfless Abzan
On Squirrels
On Risen Executioner
EDIT (Sep. 10): Corrected rule citation.
BWTeysa, Orzhov Scion Combo
GUEzuri, Claw of progress Morph
GUBSidisi, Brood tyrant
RWGisela, Blade of Goldnight Random red white cards i dont use.dec
GBLoam Pox
Modern
UBFaeries
GBWGoyfless Abzan
On Squirrels
On Risen Executioner
Right, by default cards refer to themselves when their names appear in the text box. Cards that take other cards' abilities effectively overwrite the other names with their own. The exception is when they refer to cards/permanents "named" a name, in which case it cares about a specific card name.
Example: Quicksilver Elemental says, in part, “{U}: Quicksilver Elemental gains all activated abilities of target creature until end of turn.” If it gains an ability that says “{G}: Regenerate Cudgel Troll,” activating that ability will regenerate Quicksilver Elemental, not the Cudgel Troll it gained the ability from.
RULES OF MAGIC :
http://magic.wizards.com/en/game-info/gameplay/rules-and-formats/rules