A few more things to check, i have had 4000's where the cpu slot was dirty and needed a good cleaning with Deoxit-clean the accelerator and motherboard connectors.
also its not uncommon for the pins in the cpu socket to make bad contact and i have fixed many by going behind each pin on the motherboard side with a needle to bring the contact out a bit,very delicate operation with a thin needle,but has fixed some stubborn problems.
I dont recall reading if you had checked power supply voltages. i find a4000's become flakey on boot at around 4.92v or lower on the 5v rail.
Some of the things you mention make me thinki of a bad OS install,have you tried another drive and or cf card with a fresh basic install?
The warp engine jumpers have some delayed HD booting options,are you sure the jumpers are correct? can you post a picture of the warp engine how you have it jumpered?
As for the mouse acting weird at time,this could be related to power supply issue or bad caps.. A bad CIA etc..but it almost seems software affects this from what you wrote?
