On the software end, I suggest using Thor's mmulib package. The processor library works fantastic with the TekMagic, and then you have a nice set of tools that all work together... you can do away with the supplied software entirely. (For example, I use mufastrom instead of ksremap, and mumaprom for testing kickstart images before burning.)
On the hardware side of things I've had a lot of problems.
First of all, lots of random lockups and freezes not attributable to software. My "BigFoot" PSU was full of cheap quality (and 10 years old) JPCon capacitors, so those were all replaced.
This helped significantly, but I was still encountering periodic freezes while the WB blanker was running. Same symptoms I encounter on accelerated A600/A1200's when the caps have failed. (Funny side note -- "blanker" seems to be a good hardware test, as my TekMagic would easily fly through hours of CPU intensive benchmarks (like AmigaMark), yet lock after 15 minutes of blanker, LOL.) I replaced all motherboard caps, afterward, no more freezing.
Third hardware related problem.

After 30 minutes or so, some WHDLoad games exit back to WB, returning similar errors. Pinball Dreams in particular - just let a table run, and eventually it quits to WB, more frequently as the machine warms, until it exits almost immediately. This was directly related to the +5v rail and the lower FPGA on the TekMagic.
4.95v - Pinball crashes almost immediately, warm or cold. WB is stable for hours.
5.0v - From cold, Pinball runs for 30 minutes before the errors become more and more frequent. Cool the FPGA (cooler spray), and the errors disappear for 15 minutes or so. Point a huge fan at the FPGA, and no problems at all.
At 5.15v, and a large sink on the FPGA, the errors are almost eliminated. Solder joints are all fine, and the chip barely gets warm, so it seems to be some sort of flaky component. :/ I'm confident that another small voltage increase would solve it completely, but then the unregulated +12v line becomes a little too high for my liking.
On the plus side, GVP has offered to replace both FPGAs, though I'll need to send in the card since they require programing on the board. Waiting to hear details, but I'm happy it's able to be fixed.

Do you have Burst Mode enabled?
I do, and I don't recall a difference with it off, but I haven't tried disabling it recently. I'll give it a shot and let you know if it makes any difference.