Steve Crase had Slee shave his head(sounds funny) when he re-built his 3fe, so no reason not to, he says that with the rebuild and shaved head he can go something like 20mph faster up hill, he is VERY happy. One thing to think about is, more power=more heat.....so if your cooling system in not up to par then you might find you run hot. I think Steve cured this with a new fan clutch and maybe a new rad. I went thru this on my fj60, no cooling problems with the old tired carb, re-built it(and it made a buttload more power) and then it was running a bit hot.....new rad was what it needed.
Think I read Mark Whatley shaved the head on a 3fe. Should be no issues with the computer or any sensors.
I don't know off hand what the CR is on our 3FE's (if I were to guess probably 8.5 to 1) but in general if I were contemplating this I would crunch the numbers to ensure I wasn't going any higher than a CR of about 9.5 to 1. Ok maybe 10 to 1 if I were resolved to run 93/94 octane.
Depending on how much is taken off the head, you may or may not have a pushrod length or rocker angle issue. As 60wag said .050 is no problem. On another straight six (british version of our tractor motors) I did a major shaving bumping the compression way up and had to address the rocker/pushrod issue. In that case, fabricated some rocker pedastal bushings to raise the rocker shaft by the same amout that was removed from the head. But that was way more than .050.