torque converter question

95 acclaim with 2.5L putting in a tranny from an 88 daytona, everything matches up according to the books and part numbers that i checked. my problem is when trying to connect the torque converter to the drive plate, two bolts line up, but the other two dont. Any ideas as to why it wont line up right? The transmission is tight to the block with half the bolts in the bellhousing. Otherwise is there an easy way to flush the fluid out of the other converter since it has metal shavings in it?