Most new (rebuilt) alternators will come with a regulator pack installed, but these will usually be cheapos, not good ones like Bosch, so don't expect them to last as long or perform as well under extreme conditions.
Your voltage measurement of 13.5 V at idle is okay, but the 12.9 V at 2000 rpm is indeed too low and oddly so what with that idle voltage. In my opinion that would be indicative of a worn alternator, particularly worn bearings coupled with a wear groove in the slip rings. I presume it hasn't been inspected in a few miles so suspect worn brushes as well. Note that with well worn slip rings the minimum brush length should be taken as higher than the 5mm (.2") spec which is why we normally say at least 1/4" -even more if you're going to turn the slip ring surface (I once used just a flat bastard file). Check for fore/aft play in the bearings. There should be virtually none. Note that new bearings spin smoothly, but not freely -spin a new one to feel the difference. Alternator output voltage should really be measured on the terminals on the back of the alternator, between B+ (red cable) and ground (blue cable) as well as D+ (small red) and ground. At 2000 rpm with a fully warmed engine/alternator you're looking for 13.4-14.2 V depending on temperature, electrical load and any resistance in test leads/terminals/wires. First suspect should always be the voltage regulator pack/brushes. Max diff between B+ and D+ is .5 V otherwise suspect bad diodes in the alternator. You should also measure both at the battery and the alternator to determine if there is any voltage drop due to bad cables/contacts (especially ground cabling). Max voltage drop between battery and alternator is supposed to be .25 V. Inspect the blue ground wire on the alternator. The twisted copper wire may become badly corroded, especially if the insulation isn't covering the ends completely. Cable resistance should be near zero Ohms. There are supposed to be two braided ground cables between the valve cover studs and the firewall -make sure they're intact and solidly attached at both ends.
As John suggested, it's not a bad idea to take it to a starter/alternator shop for a test. It's normally free if they smell future business. No matter where you take it, make sure you're getting a "load test".
A few months back I was chasing a mystery battery drain problem. Even died once while stopped for gas. Nary a flicker or glow on the dash alt light. After a jump it would typically be good for the rest of the day. After a bit of chasing I strongly suspected the mildly old (but not ancient) battery couldn't hold a charge. The battery shop tested it as good. I looked for mystery drains by pulling every fuse, but nothing unexpected showed up. As charging voltages both at the alternator and the battery were checking out okay, I had to suspect the alt output amperage. A visual check of the brushes and armature was okay and a shop load tested it at exactly 100 amps. The bearings were starting to get worn, but nothing abnormal. Even though I didn't find a horrible voltage drop across the blue alt ground cable, it was corroded so I subbed a spare and cleaned up all the engine ground contacts including the braided cable between the valve cover studs and the firewall and removed the intake manifold brace for a surface cleaning (both ends). End of problem. The battery simply wasn't getting enough of a charge to hold it for the occasional 7-10 days the car might have sat idle -I was often just using the other 940 as it was often first in line out the driveway and sucks less gas on the highway. I think I didn't spot the voltage drop because I was always testing on dry days and not on damp days where intermittent ground problems can surface.
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Dave -940's, prev 740/240/140/120 You'd think I'd have learned by now
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