if you have been keeping up with your Windows Updates, one of them, Security Update 811493 has the side effect of slowing down the boot up sequence.
As this patch is only required in the case where "An attacker has the ability to log onto the computer locally to carry out an attack." (to quote the microsoft 'blurb') this does not apply to most home computers, so you can remove it. I did so on mine and noticed an improvement in the bootup time.
NOTE. This is only one possible cause of the problem.
What do you call slow bootup? I have just tried my Win98 from switch on till I can start running programs of 1 minute 40 seconds. I'm not sure if this is typical or not, but it may give you a base line to gauge the bootup speed against.