Should not be any difference between the 98 and 99, 00 was the spark plug rail and no distributor setup. About the only difference I can picture *might* be plugs on the harness *maybe*. Before I stuck the new engine in though I'd do the O rings on the oil filter mounting boss.
Someone here also had an issue with a new exhaust manifold not fitting correctly with bolts, about a month or two ago, I just remember him not being able to get a seal on a couple of the ports, he had pics too...it was supposed to be a direct fit manifold and as I think about it the flange was either thinner or thicker than what came off, forget which now. Sorry, thats about all I can think of at the moment..
Actually while you have it out I'd also replace all the freeze plugs with brass ones, easy to do now, harder later. Give the engine the once over and look at it from the perspective of having to do it with the engine in, pay attention to the oil gallery plug on the back of the block, the one thats covered by the bell housing, if there is ANY oil back there or even greasy dirt I'd replace that one in a hearbeat. Might even be a good time to stick a block heater in there, easy now, hard later...