My question is about the correct position to install the oil pump/ distributor shaft. I have the motor at TDC, and installed the slot in the gear parallel to the camshaft. When I put my MSD distributor, it does not point to # 1. what am I doing wrong?
Thanks

Where does it point ?

Some dizzys have a different bottom tang to top rotor phasing so one dist might be right but drop in a diff one without disturbing the inter gear clocking and the rotor will be in a different position. Just lift the inter gear/shaft & reclock it till the rotor points at #1 & you're good and not required but I like to maintain the OE factory #1 wire position in the cap as it makes it less likely to make a mistake down the line and it lets the wires nestle the neatest with the shortest lengths possible so I start #1 wire per the book then reclock the gear wherever it needs to be to achieve that routing

If the slot in the gear parellels the camshaft and it is on TDC of the firing stroke the rotor should end up pointing at around 4 O clock looking down on the ditributor from the passenger side fender I try to follow the OE way Mopar index the disrtibutors with # 1 below the front distribuotr cap holdown, positioned around 4 oclock As already siad you can make the motor run with the slot at 90 degrees to the cam as long as the firing order is starting where the distributor rotor is pointing at that place on the cap where #1 spark plug wire is when #1 is at TDC on the firing stroke I've seen B,RB and 426 Hemi motors wired a whole bunch of different ways

The "correct" way is to have the engine at #1 TDC and install the distributor gear with the slot parralleling the camshaft. It won't be "absolutely" in line with the cam, but cocked slightly towards #1 cylinder. If you get it too far off parrallel, it can be hard to set the timing as the distributor advance may hit things.