I like Fel Pro gaskets, and usually gasket match the intake to them, and try to line it up as well as I can, to the head without removing and disassembling them. but then again I may be totally wrong with what I do, since I'm sure someone will know more, and have a better way of doing it.
What heads are you running? Matching to your intake is a good idea but you also need to match to heads. I'll have to look it up but I wrote down a fel pro intake gasket that worked will with my gt40s and torker intake.
I'm partial to Mr. Gasket Ultra Seals. If your talking about the Fel-Pros with the rubber around the ports, I've seen several cases (me included) where the rubber pushed out of place and caused leaks.
Nothing wrong with port matching an intake to gaskets.. so long as you observe and stay within the heads inlet port dimensions and avoid obstructions. Not sure what size the stock 289 inlets are.. and too lazy to look right now.. but the chances are that they may be too small to match up to a gasket matched intake. I usually shoot for around .020-.030 smaller intake manifold port exits compared to the heads inlet size to aid in easier placement variations and avoid doweling requirements.
FelPro 1250 intake gaskets for the smaller 289 ports. The 1262 are for bigger ports. I always use black silicone around the un-gasketed areas at the water port at the front of the heads and across the ends of the block. I never use the rubber or cork block pieces. SPark