1. You need to determine how much current you are going to be sinking. In your previous thread, someone linked you to AN293. That app note shows that MAX II can sink up to 130 mA between GNDIO pads.
You must look at the EPM240 full I/O pin list to understand where the GNDIO pads are. They are listed in the Pin/Pad function column of the full pin-out. AN 293 indicates that you can only sink 130 mA total for the set of I/O pins located between any two GNDIO pads in the list.
If you know you are sinking 25 mA per pin, then you can only have 25 mA x 5 pins = 125 mA for driving LEDs between any two GNDIO pads to meet the 130 mA maximum limit. So you must make sure you distribute these around between different GNDIO sets if you have 16 pins at 25 mA. If you have only 5 mA, then you don't need to worry about any restriction since 5 ma x 16 = 90 mA total.
2. Check the online store at
www.buyaltera.com (
http://www.buyaltera.com). Click MAX II, then do a search for EPM240 so you can see the different flavors and costs. Slowest speed grade is cheapest (-3, -4, -5 means -5 is the slowest). EPM240G is a 1.8V device while EPM240 (non-G) is a 3.3V or 2.5V device, same price for EPM240 size. Smaller packages are are cheaper - the EPM240 only comes in 100 pin packages so the prices are generally the same for given speed grade across the packages. T100 (TQFP) is the easiest to use for assembly and board layout.
3. JTAG pins are fixed on the device, you need to check pinout for their location or check the .pin file that results from Quartus. It shows how to connect pins.
For pull-ups and other JTAG considerations look at pages 5-8 on this guideline document. It also talks about the current sink.
http://www.altera.com/literature/an/an428.pdf