If you're going to use IR as the origin sensor, be sure to shield it from ambient light and keep it clean if you use a coolant.
Use a coolant!- especially with soft metals. Even WD-40 is better than nothing. I have scrap to back me up on this!

Look into an encoder or laser. Lexmark (and other printers) have very nice encoders and strips you can hack and integrate for position feedback.

I presently use the corner of my vise as the origin and get the accuacy I need. Use a $10.00 edge finder
(http://www.mscdirect.com) to find the inner surface of the vice jaw for the Y and the left hand side of the vice jaw for the X then set that as your 0-origin in your program. When you place the part in the vice, the Y is inherently zeroed and the x can be set by aligning the edge of the part with the edge of the vise using a piece of hard smooth material. This is accurate and repeatable.

The smaller the whole, the higher the RPM. Mass production PCB drills run at around 8KRPM. Use coolant.

I use a bridgeport and coolant. An off the shelf drill press will rarely give you .001" in accuracy but you'll get a .040" hole in a .100" solder pad with enough surface for a good connection. Use/make a bigger pad if you can.

If you drill stacked parts, the material from the lower part will be pulled up between the parts and cause the topmost part to distort - giving you an oversized or almost triangular hole in the top part.
Take a piece of PCB material and drill oversize holes in the same position(s) as the holes in the part you want to keep. Put the oversized part in between the keeper parts and you will have little pockets for the chips. This will prevent the distortion and also give you excellent support around the holes you are drilling.

If you can, drill a whole in the middle of the part first (you can use this as a mounting hole in the finished part) and screw all the parts together, this will prevent pullup in and near the center of the part when you drill the holes for the components.

Did I mention using coolant? :-) "Tap Magic" is great but WD-40 will be OK.

If you knew all this, sorry. If you didn't, I have finally contributed *something* to a forum that has been incredibly helpful to me!!!