Hi Moe,
First you need to convert the Allen 301 to a MIDI controller. Second you build a Hauptwerk sound engine and third you connect the Hauptwerk sound engine to an audio system.
Converting the Allen 301 to a MIDI controller:
If you really want to keep the Allen stop action you maybe can convert the keyboards and pedal board to MIDI with boards from Harrison Labs. Here is an example from eBay.
http://www.ebay.com/itm/MIDI-KEYBOARD-A ... 2c679fe97b The stop action and the expression pedals are not included in this conversion. I have never used these boards and have no affiliation with the company.
It may be more cost/labor effective to remove all of the old Allen analog electronics and put an encoder on each of the keyboards and pedal board, convert the pistons to MIDI, convert or replace the expression pedals and use a conventional KVM to program the pistons. It appears to be possible to use the original SAMs and stop tabs using an Artisan uMIDI system and the Allen power supply but the nomenclature on the tabs will not match the various organs in Hauptwerk unless you get them engraved to match a particular sample set and do not change sample sets.
Building the Hauptwerk sound engine:
There are several people on the forum that can supply you with a proven sound engine. If you want to build it yourself, I recommend an i7-6core CPU in an x99 motherboard with 32GB of RAM and storage to your liking. The current value champion in audio modules is the Behringer FCA610 used with a Texas Instruments IEEE-1394b card.
Using the Allen audio system
I have used the Allen amplifiers and speakers in a church installation and it appears that the amplifiers and speakers are 'made for each other' as other speakers hooked to the Allen amps did not sound as good as the Allen speakers and vice versa. If you have just two speakers and amps it would be a good idea to collect another 4 sets of amplifiers and speakers identical to the ones you have. This would allow for a six speaker system which would sound great with Hauptwerk.
If you have not seen Kenneth Spencer's book "All about Hauptwerk", please try and get a copy.
There are several companies who do this type of conversion also. PM me if you want more information on them.
Best regards,
Thomas