Tremulous is an actual mod of baseq3 isn't it, it still uses baseq3? If that's the case then yeah, you're going to be stuck if you continue with what you have. As you've rightly noted, the number of entities is causing the compiler/engine to bug out - iirc the limit is 1024 so your using 998 isn't leaving the game enough 'space' to add all the dynamic content it needs to generate on the fly, bullet hits, shell casings, rocket models and so on, ideally you shouldn't let your entity count (models are 'entities') go to far above 700, definitely not over 800 and most certainly not over 900.
As lifting the limits isn't going to be possible based on Tremulous being a mod of baseq3 what I'd suggest doing is looking into ways to get that model count down, you're going to need to strip out at least 200 of them. So... if this is a terrain map and you have lots of trees, try combining groups of them together into fewer larger units, instead of 400 individual trees you have 100 groups of four (where four trees are combined into a single model).
Look at your entity count as well, spawn points and so on, knock those back if you can. The number of brush-based entities can also problematic so make sure you're only using exactly what you need. Check your brush count as well and see if you can combine/optimise - but watch out for shader overflow by using too many unique surfaces. And finally make sure you're building using the "caulk hull" process so only 'structural' brushwork splits the BSP.
Must be a big level!
