Hi Rich,
Well I would say the pickup height will give you more power output due to the closer magnetic field to the strings but the tone itself I would not expect much difference. Different pickups have their on tonal differences from one brand to another and from different type magnets, the guage of the copper wire windings, and the number of turns which vary the resistance in the signal.

Usually I can find the same tones from one humbucker pickup to another. The capacitors in the signal line from the tone control pots can make a noticeable difference as well. The same amp may need to change settings to accomodate what you want to hear. Another big deal here to consider is the wood the guitar is made of and the neck also. Even fretboards can vary the sound. The Less Paul standards usually came with rosewood fretboards wheras the Less Paul customs came with ebony fretboards.

Even the Les Paul custom fretless wonder guitars that had the tiny, almost no frets at all, had a more mushy tone simply because you were getting very little tone from the fret wire at all. The jumbo frets gave a more metalic sound due to much more metal and more sustain. All of these things will factor into the tonal capabilities of a guitar. It is really the sum total of everything that sets the tones. The strings also play a big part in this.

I was an Alman Brothers fan and still am. I would think there is a way to EQ what you have to match the sound. You can find humbucker pickups that are more vintage sounding than the later ones. Most music stores would be able help you I think and can get the pickups and usually they have someone to install them for you. I refer people a lot to a company called Stewart Macdonald. He has a lot of special pickups including vintage style pickups.
His website is http://www.stewmac.com
I hope this will help you.

Rick Andrews, Andrews Guitar