The timing belt job didn't quite go as smoothly as planned!

I found a pipe & small container to use as tools for tapping the new front engine seals in. However, the crank shaft seal was resistant so I gave the container a good push only to watch the seal go WAY in, probably recessed 1/2 inch.

Upon seeing the oil passage ways exposed I realized my error & promptly removed the seal (destroyed in the process of coarse). I'll go pick up a new crank seal on Monday. See the following with regard to shaft alignment.

So, Can I assume the cam seal & intermediate shaft seals do not have these oil passages meaning that a slight recess of say .1" will do no harm?

Also I noted that although all three shafts line up with the timing marks, at # 1 TDC the rotor is not exactly centered on the plug wire for # 1 plug. It is slightly advanced toward the next plug wire (#3)even though it probably has some electrical contact.

So I am wondering if the spark happens just before tdc, or should I cheet the intermediate shaft slightly to center the rotor on # 1 plug wire when the cam & crank both line up with the timing marks?

By the way, I'm still looking for the smoking gun that causes poor performance & a stumbling idle condition so am wondering if this could be a contributor.

Thanks

Mike
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1988 245, 237K mi, 5 speed