When you install the converter you are aligning the hub, the input shaft splines, and the lock up clutch splines- it may take some twisting back and forth with some pressure into the trans to get them all to line up.
Copied some install info which may help you- gives a good what to check list :
The following must be checked and replaced, if needed on all automatic and standard transmissions where applicable
CONVERTER INSTALLATION:- Make sure the converter is all the way into pump gear-don't assume its in place when you receive the transmission. After you are sure it is in place, always keep tail end of transmission low so it cannot slip out. This is the #1 cause of failure at time of installation, or soon thereafter.
Important Torque Converter Installation Tips
1) PREPARE THE CRANKSHAFT AND CONVERTER FOR INSTALLATION a) always check crankshaft for burrs and out of round b) remove rust with emery and lightly grease pocket c) remove paint from converter crank pilot with emery d) pour one quart of ATF into the converter e) check the flex plate for cracks and worn teeth f) install the converter on front of the transmission
2) CHECK CONVERTER TO FLEX PLATE ALIGNMENT a) after bell housing bolts are tight, then check free movement of converter. It should have 1/16 to 1/8" of clearance between pads on converter and flex plate. If you have more than 1/16 to 1/8", install equal thickness washers to reduce clearance to 1/16 to 1/8". If not enough clearance, remove transmission and check to see if converter is seated in front pump properly. b) draw converter bolts up evenly so as not to pull converter into a bind causing vibration and pump bushing failure. c) if vibration occurs after installation, mark converter to flex plate and rotate the converter one bolt hole at a time.
3) The number 1 cause of vibration is failure to prepare the crankshaft for installation. Each time the converter is installed without sanding out the crankshaft rust, removing the paint from converter pilot and adding a little grease the converter may be drawn up crooked with the first bolt, causing the converter to run-out and usually ruining the pump bushing. The 2nd most common complaint on converters is a whine after installation. This usually means too much clearance between converter pads and flex plate. This draws the converter hub too far out of the pump drive gear causing the gear to rock .
CONVERTER WHEN NOT REPLACED:- Must be removed and thoroughly flushed. Make the following inspections: thrust washers for misalignment, condition of inner sprag, hub condition for wear and mounting devices to insure proper alignment.
COOLER AND COOLER LINES: - Must be flushed to remove all metal particles and oil. Don't just blow out with air. Use a solvent that will flush out old oil and metal particles.
FLEX PLATE: - Inspect for cracks where plate bolts to engine and out of round holes where converter bolts to flex plate.
MANUAL CONTROL LINKAGE: - Must be re-adjusted to assure proper settings for unit being installed. Adjust linkage with car in actual road operation.
MOTOR AND TRANSMISSION MOUNTS: - Their condition will affect linkage adjustment and cause excessive wear to internal transmission parts if worn. Also, broken or oil-soaked mounts must be replaced.
U-JOINTS AND DRIVE SHAFT YOKE: - Rough and worn u-joints may cause vibration in drive line and failure of bushings and seal in tail casting. Rough or worn (tapered) front yoke will quickly damage rear seal and bushing, causing loss of lubricant which can lead to transmission failure.
ENGINE: - Many transmissions depend on engine vacuum for proper shift pattern. Good engine performance is a must to insure proper vacuum. If engine vacuum is too low it may cause the transmission to have a short life.
DO NOT: - Check out transmissions operation with the drive wheels off the ground.
DO NOT: - Re-use old oil. Dirty oil causes valves to stick and may clog lines if contaminated, both may lead to premature failure.
SHIFTER PLATE AND SHIFTER FINGERS: - Because of the various styles of shifter controls it is impossible to always supply the transmission with the proper shifter plate. It is of great importance if the shift fingers indicate any wear they must be changed. Worn fingers may cause too much gear movement resulting in noisy gears or improper synchronizer application. Shift arms must be the exact kind as on the original transmission.
SHIFTER LINKAGE: - Excessive wear of shifter linkage in shifter tube (in steering column) may cause malfunction in shifting. Too much wear at these points may cause improper throw or movement of the desired gear at the proper time. Sloppy shifter at steering column, dragging effect, in or out of gears or jumping out of gear all indicate possible linkage trouble.
CLUTCH UNIT AND PILOT BEARING: - The clutch must completely disengage to properly engage first or reveres gear. The condition of the pilot bushing will determine how well the transmissions front shaft is supported and how freely the clutch disc will operate.
DO NOT ASSUME THE ABOVE ITEMS ARE GOOD. CHECK EACH ONE THOROUGHLY.