Satch_999's post in Tracon: arrivals come in from center at low altitudes was marked as the answer
My advice would be to use Notepad ++ for editing (http://notepad-plus-plus.org/)
In this case you must make a bakup of your KJFK.asx file
Then open it with Notepad ++ and look for "star route".
You should see somthing like this: ( this one is taking from my own made EHAM sector)
<object id="0" name="TOPPA2A" type="star route" lat="52.315399" lon="4.790200" alt="5000.000000" rot="0.000000" len="0.000000" donthide="0" params="EHAM:36L
EHAM:36C
EHAM:36R
EHAM:18L
EHAM:18C
EHAM:18R
EHAM:27
EHAM:09
EHAM:24
EHAM:06
EHAM:04
EHAM:22" knotsnum="0">
<section name="waypoint_to_waypoint" strlat="53.398022" strlon="3.565222" endlat="52.759289" endlon="3.745359" stralt="0.000000" strlat="53.398022" endalt="0.000000" alt="18000.000000" marker="0"/>
<section name="waypoint_to_waypoint" strlat="52.759289" strlon="3.745359" endlat="52.571850" endlon="3.778223" stralt="0.000000" strlat="52.759289" endalt="0.000000" alt="15000.000000" marker="0"/>
<section name="waypoint_to_waypoint" strlat="52.571850" strlon="3.778223" endlat="52.526119" endlon="3.965922" stralt="0.000000" strlat="52.571850" endalt="0.000000" alt="11000.000000" marker="0"/>
Where the text is highlighted red in this post, you can change the altitude at the waypoint.