The Z-fares on the KUL-CGK tag are quite affordable at around USD200. The cheapest economy fare sets you back USD100. Loads vary depending on the day of the week, and tend to be heavier during the weekend.

As for the lounge, the MH lounge will also accept KL Business pax, although KLM uses a different lounge. MH's Golden Club lounge is really nice.

The only benefit of flying MH then is the schedule and frequency. MH is operating 3 daily flights vs. KLM's one, and therefore offers a better choice of timings. KLM's CGK-KUL sector arrives quite late at KUL, but still in time to catch the KLIA airport express.

Comfort wise, MH operates at least twice A333s, which aren't all that much to talk about in terms of cabin comfort. The middle flight is often operated with the A332, which is much more comfortable in C. That said, MH is way more expensive.

I'd go for a KL Z-fare.