If you have an EF level you are comfortable with, don't think of it as "investments". It should be considered a completely different pot of money and not be included in your retirement asset allocations at all.
Are you worried that you should decrease your emergency fund? One of the problems that EFs have is the paucity of tax sheltered options to keep them in. There's I Bonds and munis and that's about it. If you have the space in your 401k and the cash you might want to work something like this:
Worst case scenario in a crash (discounting a Black Swan, natch) your stocks lose half their value. What some people do is figure out what amount they want to hold in an EF and multiply it by 1.5-2x. They put this into stocks in their taxable space. They hold their true EF in conservative bonds in their tax sheltered space. Should an emergency arise, they sell stock to cover it, then as soon as possible swap that amount of bonds for stock in the 401k. You risk very little doing this and may even be able to take advantage of tax loss harvesting.
If you want specific portfolio advice you can follow the directions here:
http://www.bogleheads.org/forum/viewtopic.php?f=1&t=6212
It can be quite an education!