I went the other way... I had a 4 speed and swapped in a 5 speed Isuzu on my 86 V6. For me it made no difference whatsoever except that the ECM (PROM/CALPAK really) has no idea that there's another gear after fourth so it doesn't tell me to upshift into fifth

. The shift light information isn't used for anything except to turn on the light on in manual cars (on autos it's a different story since it uses the signal to switch the TCC on and off). I don't believe there are any noteworthy differences that will adversely affect the performance or operation of the ECM or engine. It hasn't in mine.
The VSS gear however might need to be changed to keep the speedo correct. You can use this chart to help determine which color gear you should use to maintain speedo calibration. It's a little awkward to use but if you start by looking up your tire size on the lower table, then find the correct axle ratio and transmisison you are installing, then find the letter code for the "driven gear" you should be using (should be a "N" or an "O"), then look up either N or O in the upper table under the "driven gear" column and see what color gear that corresponds to. If you get lost, just shoot me a PM and I'll help you some more.