If you mill them you'll have to get different lenth pushrods.. But you should check them when installing a cam or putting new rockers on anyways.. If you deck the block, basicly doing anything to change valvetrain geometry...
I wouldnt mess with milling though, unless the heads are gasket etched, warped or something ( remember though, if the heads are warped, and your not rebuilding the engine and cant check the deck, think hard about doing anything, because the head could be warped to the conture of the block deck and cause more probs than it solves and can lead to cracked heads! ), even then I'd only do it enough to take out the etching.. If I remember right, the compression ratio on 318's and 360's stock is 9:7.1, which is plently high.. Unless you like running high octane fuel, and possibly even having to add octane booster.. Part of the reason our trucks detonate so bad is the compression ratio.. Other vehicles ( take some Ford engines for example ) have knock sensors to adjust timing when they detonate, our trucks dont.. You could move the crank sensor back to decrease ignition timing 3-4 degree's though..
As far as aftermarket heads, always a good upgrade.. For me, if I had a set of stock heads that just needed a valve job and all the SIMPLE stuff, I'd put a little extra money in them.. When it comes to adding guides, valves, and all that jazz, I look into new heads. If I have the money to spend then I dont even think about messing with stock heads. Ofcourse unless it's a junker that I dont care about, just toss the stockers back on.. And while the heads are off, taken apart and clean, I always try to find the time to gasket match and knock the casting flash out.. Just like deburring a engine block, I do it just to prevent cracking or the possibilty of it breaking off and sending casting sand through the sys...
If it was my truck, I'd try porting them.. Even if they might crack. I would do it now too, but this engine has to many miles on it to even screw with, might be just fine, or it may open up a can of worms. Think about it, these heads STOCK are prone to cracking.. It's just a matter of time, with any head really.. I just wonder if it's the stress of being loosed back up, then torqued back down thats causing them to crack. Think about it, where the head bolts are, they do cause those area's stress, as with every engine. I dont know, but where these heads are cracking I dont see how slight port work will cause them to crack, simply because if you do it right your really not in the area where they are cracking, between the intake and exhaust valves.. I have seen a few heads crack in that area before, and it was because they ported them to far, far enough that it was hurting performance rather than improving it. Some so far they left nothing but paper thin material between the exhaust port and a water port, then cracking or busting out from pressure and heat then pumping water in the exhaust port ( or intake ). If anyone has any info proving me wrong tell me, cuz this is just how I see it and my experience, I dont mind being corrected.... Didnt mean for this post to be so long, just trying mention what I know on the subject..