Use a toothpick or something,  then align the oil pump shaft so the housing can properly seat,  check tdc and the holes aligned on the cmp and tight the clamp on the housing,  put the cmp back and you are ready to go. 

 I could be wrong and I've been known to make things up but I just did this with a MS906TS.  My steps to doing this were simple on a 2004 TJ I6.  After I set #1 piston at TDC on the compression stroke (very important) I installed the oil pump drive gear (OPDG) with new cam sensor on top with it's alignment pin installed.  I ensured the connector was pointed straight back as best as I could while ensuring the oil pump was properly engaged.  Removed the alignment pin from the cam sensor.  Warm the engine up to operating temperature.

I had already connected my AUTEL and navigated to the vehicle on the "Select diagnostic type" screen.  My next steps were as follows:

Manual selection

Year

TJ-Wrangler

Diagnosis

Control unit

Powertrain

ECM(Engine Control Module)

Special function

Set synchronization signal (if the engine is not running you are likely to receive the "Engine must be running to carry out this function" message - touch OK if it is running)

[you should hear the engine accelerate]

The screen will display:

Set sync spec = 0^o

Distributor setting = (current live value)

Current synchronization status: (In range or out)

Loosen the retaining clamp bolt just enough to move the OPDG and adjust slightly until you receive the best reading possible on "Distributor setting = (current live value)".  Carefully, re-tighten the retaining clamp bolt while paying attention to the AUTEL setting to ensure it doesn't go out of spec again.