Thanks much for taking the time to help me with these problems.
I did finally resolve most of the issues.
First I erroneously stated that the oscillator was of the colpitts configuration. It is not. It is the pierce configuration, and I do and did have the xclks pin pulled low using a 10K resistor.
The problems with the clock were being caused by a floating vregen pin, which when connected to Vdd, eliminated that problem. Surprisingly the older MC9S12A128CPVE (Motorola Logo) worked fine in spite of vregen floating. With the newer MC9S12A256CPVE (Freescale Logo) some worked, and some had 0 Volts on the 2.5 V pins.
I stated in an earlier post that /irq and /xirq were high out of reset. This tured out to be true only part of the time. at other times they were around 1.7volts, but in either case the parts malfunctioned except fot the older parts having the Motorola Logo.
On all of the newer MC9S12A256CPVE (Freescale Logo) the first line of assembly code needed to be a write pucr, enabling the internal pullup resistors for port e (pupee). On the pierce hardware, this was all that was necessary to facilitate correct operation. On the P&E DEV9S12A/B with the canned oscillator it was necessary to do this and to add 10K pullups to both /irq and /xirq.
I did not test all of the newer parts uniformly as I do not have zif or clamshell sockets, and need to desolder and re solder to do this, so some may behave a little differently.
A problem with the pierce hardware is that if I connect the external pullup resistors to /irq and /xirq, then one of them will not work with the out of reset conditions. I did not try changing the irqen register contents yet to fix this. If I leave the external pullups out of this circuit, and activate the internal pullups via pucr/pupee, then it works normally, and both /irq and /xirq function. I did not try all of the modes on the DEV9S12A/B, and did not identify which interrupt failed to work on the pierce hardware. For my current product, I do not use /irq or /xirq.
The only problem remaining to be resolved is that when using P&E ICDS12 and executing it's target hardware reset command, the target hardware will then halt with the program counter at $0001, instead of running at full clock speed and displaying watch variables as it's supposed to unless the power to the target hardware is cycled off then on again each time the command is invoked. Currently P&E is investigating this for me, but you may have some other suggestions.
Again many thanks to all who have read, considered, and(or) answered this post. 