Hooked batteries up in series ( 24 volts ) now

It could be you have a fault in the Diode pack in the alternator you need to get this checked at an alternator repair center.

Your alternator may not be putting out enough. Take it off and have it tested. If you have a digital volt meter you should have just over 13 volts at idle and at higher RPM top out around 14.4 volts at the battery.
You may also have something draining the battery. Is there a large strong spark when you make the last connection (the negative should be hooked up last)? You may get a light, small, faint spark from the ECM drawing power.

check your spark plugs see if they are wet with gas. otherwise turn your dist 180 degrees.

This won't actually give you 24 volts... All this will do is give you more amps in a traditional circuit. You could run them in a series.... but I wouldn't recommend that. Those batteries are built to provide 12 volts. What do you need 24 volts for?

actually you can.. check this blog from fords website the ecc relay bypass for testing purposes only

http://www.ford-forums.com/ford-pick-up/13239-1991-f-150-no-fuel.html

I would try to read the resistance between the battery cables(plus and minus) with the battery totally disconnected and the key in run position and see if it is <=150 ohms(considered a short).

A 12 volt battery is actually 13.2 volts fully charged. If you are reading 16 volts, you are probably getting extranious voltage from the system somewhere, especially if the vehicle is running when you check the voltage. The alternator will put out about 15-18 volts to charge the battery normally, and yours may put out 28-32 volts to charge them in series, but the batteries, when disconnected, should never read more than about 13.2 volts each. Typically, it will read about 12 1/2 volts when disconnected. COMPLETELY DISCONNECT BOTH OF THE BATTERIES. If you still read 16 volts when it is disconnected, you must have a bad meter because the battery can't produce that much voltage, no matter what. (Six 2.2 volt cells connected in series inside the case.) Put the meter on a known good battery on another car that is not running and see if you get the same reading. It sounds like the other battery is almost dead, regardless, and it sounds like your series/parallel switch may be malfunctioning. (That is the switch that puts the battery in series to run the 24 volt starter, then puts the batteries in parallel to run the remainder of the vehicle on 12 volts. This is all assuming that you have a diesel vehicle with a 24 volt starter and that is why you have two batteries.

It sounds like a short somewhere in wiring draining your battery. You might try a different alternator it mite be faulty