> Kinetis (wish I were working with that; seems like support for it is more mature).
Support is a reason to choose one family of chips over another.
Did you find AN4254? It details motor control on a Tower system using an MCF5441x, but assumes you're using MQX. Depending on how much your time is worth, MQX may be worthwhile.
> I still do not have output on the pins
It would help if you said which pins you're monitoring and expecting to toggle, and whether they're "CPU Pins" or some connector or test point on the Tower board.
The MCF5441x has eight PWM outputs, PWMA0-3 and PWMB0-3.
Signal Name GPIO Alternate 1 Alternate 2
SDHC_CLK PG5 PWM_A0 DSPI1_SCK
SDHC_DAT3 PF2 PWM_A1 DSPI1_PCS0
SDHC_DAT1 PF0 PWM_A2 DSPI1_PCS1
UART2_RXD PE4 PWM_A3 SSI1_RXD
SDHC_CMD PG6 PWM_B0 DSPI1_SIN
SDHC_DAT2 PF1 PWM_B1 DSPI1_PCS2
SDHC_DAT0 PG7 PWM_B2 DSPI1_SOUT
UART2_TXD PE3 PWM_B3 SSI1_TXD
On the Tower board, the four "SDHC_DATn" ones are marked "SDHC_DAT[3:0]" on the board. The other two SDHC ones are CMD and CLK pins. The remaining two PWM signals are U2RXD and U2TX.D.
I don't have a Tower system, only one schematic, so I don't know what access you have for these pins, and what they're pinned out to or connected to. They may be connected to an SDHC card socket for all I know, or perhaps that's an option.
Back to the CPU. The PWM signals are all "Alternate 1" connections to these pins. If you're used to simpler CPUs (like the 8-bitters), then the selection of which function is connected to which pin depends on which peripheral is enabled. If you enable the UART (for instance) then it "owns" the pins, otherwise they're GPIO. On all ColdFire CPUs except for the MCF41 ones you have to explicitly program what device is using the pin.
For PWM_A3 and PWM_B3 you have to program "15.3.6.8 UARTn Pin Assignment Registers (PAR_UARTn)". For the other ones you have to program "15.3.6.9 eSDHC Pin Assignment Registers (PAR_SDHCH & PAR_SDHCL)".
On some CPUs, every I/O pin on the CPU has a separate register. They take a lot of programming (or setting up of tables) to get going.
You may have already done all of the above and it may not be working for some other reason, but the above is my first guess from your posts.
Tom