The best manual for the 90-30 instruction set is still the one they published for the DOS-based software. You can download it here:
http://www.gefanuc.com/support/plc/m-lm90.htm
The publication number is GFK-0467L
The equivalent instruction to the AB JSR is a subroutine CALL. The icon for it looks like a person shouting. You can also find it the dropdown list of functions. It's under the heading 'Control'. Before you can CALL a subroutine, you must first add the subroutine name to the project. Right click on the folder browser, select 'New', then 'Subroutine', and then select your language preference (either ladder or instruction list). Fill in the name for your subroutine and you're ready to go.
Data from analog input modules will be in %AI memory. You determine the specific addresses in the configuration. The raw data will have a range of +/- 32000. For example, if you have an analog input channel configured as 0 - 10 volts addressed to %AI001, then at zero volts, the value in %AI001 will be zero; at ten volts, the value in %AI001 will be 32000.
Timers and counters don't have an assigned data type as in AB (there is no equivalent to T4:1). Instead, each timer or counter uses three consecutive %R addresses. The first of these is the accumulated value (equivalent to T4:1.ACC). The second is the preset (T4:1.PRE). The third is a control word. Bit 16 is the equivalent to T4:1.TT. Bit 15 is the equivalent to T4:1.DN. Rather than trying to extract the 'done' bit from the control word, most people just put a coil instruction at the output of the function block and use contacts from that coil as the 'done' bit.
Whatever else you do with timers, make sure that you don't overlap the %R addresses. By that I mean, don't program one timer using %R001 as the first register address and then program another timer with %R002 as the first register address. The timers will not work properly if you do, and it can be frustrating to debug. There is a way to avoid overlaps. When you are programming a timer, and you are prompted to enter the starting %R address, instead of entering a specific address like %R101, just enter %R. VP will select the next unused %R address.