The converter is the least of your worries and odds are the transmission is on the way out based on the useage, CEL illuminated, performance issues, and the rotten fluid.
It could be grey and nasty due to engine coolant from a leaking trans fluid cooler or due to heavy contamination from aluminum; or both.
The fluid is probably puking out of a vent and a slipping transmission can overheat the fluid and cause this problem.
At some point (not known to me for sure) there's a special adapter plate needed to align the torque converter on these transmissions but I cannot remember if a 98 fell into that category or not. If the converter is removed or dislodged (during the engine swap?) and the adapter is not used the front pump seal may leak.
I'd get an independent transmission shop (NOT MAACO, Cottman's, etc) and have them scan it and take a l