I've had an Ibanez SA260FM for quite a few years. It has a five switch selector, a tone push/pull pot, and three pickups. I had an SH-6 put in quite a few years ago by a professional. The middle pickup had never worked until I decided to fix it myself recently. In fixing the middle pickup's wiring I noticed that the switch selector is messed up.

Let's say position 1 is only neck, and 5 is only bridge.

Position 1 works properly. uses only neck
Position 2 uses all 3 pickups
Position 3/middle uses middle and bridge
Position 4 same as position 3
Position 5/bridge uses bridge

As well the push/pull pot seems to be backwards as it sounds like the full humbucker is engaged when the pot is pulled up (this has been a problem since I got the SH-6 originally put in, but it never bothered me until now).

Any help would be great, thanks.
Sounds like the person may have buggered up the wiring during the install. If you're able to check for yourself, this is the wiring diagram from Ibanez for the 260FM. I would verify if everything is wired to the switch and the push/pull pot properly.

Diagram: http://www2.ibanez.com/supportResources/wiring/2006/SA260FM.pdf

Keep in mind, the wire colors from your SD HB might be a bit different to the Ibanez one.
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Use this to translate the wire colors from Ibanez to SD - https://www.ultimate-guitar.com/forum/showthread.php?t=1681767
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