Of course you could use your imagination and come up with what you think is best. It is a game of imagination after all................aint it?
Anywhoo, the MM should be out by months end, so converting anything might be an exercise in killing time I would think.
Sure, but there are often unique creatures in adventures as well as creatures the MM will not cover. In my Age of Worms conversion, there is a lurking strangler, an allip, wind warriors, small elementals, mad slasher, chokers, troglodyte and bugbear zombies, a lesser aspect of a god, an assassin vine and a spawn of Kyuss. Since I do not have a MM, those are guesses as to what is not in the MM. Those are just in the first 3 chapters of the adventure path. I am totally looking forward to the MM because it means that the majority of creatures in an adventure are covered. I imagine we will get some solid guidelines for creating creatures and assigning a CR in the DMG.
To the OP: As for converting 3.5 encounters to 5e, I recommend looking at what difficulty the encounter as a whole is supposed to be. Use the XP guidelines for an encounter of a party that level and the number of people in your party. So if you have a 5th level party of 5 adventurers and the EL of the encounter is 7, look at the encounter guidelines for a moderate difficulty encounter for a 5 member party of level 7. That would be 3500XP, which is a challenging encounter for a level 5 (the party's actual level) party of that size. Then fill the encounter with the called for creatures using the MM, keeping in mind that the XP cost multiplies as you add creatures. If a creature does not exist in the MM, look for a creature that behaves similarly (fighting lurking wizard, etc.) of the same CR. Replace that creature's armor, abilities, traits and actions with appropriate things for the creature you are converting. Ability scores generally just copy over. If the creature has armor, find an equivalent armor from the equipment table in the PHB, but natural armor bonuses should possibly be reduced. Find equivalent weapons from the equipment chapter if necessary. The hardest part is converting the special abilities. When possible, copy over a similar ability from another creature in the MM or follow the general feel of the effects of other creatures in the MM. For example, the allip has a wisdom damaging attack if someone magically contacts its mind. Another creature in 5e does ability score damage that recovers after a short rest. So you could have this trait do 1d4 Wisdom damage that can be restored after a short rest.
Since many creatures have a different CR in 3.5 versus 5e, starting on the difficulty for the encounter and filling it with the called for creatures (which can be of a different CR than in 5e) will allow you to quickly convert the encounter while keeping the proper feel. One thing not to do: If a creature in the encounter is called for at a CR higher than the party's level, strongly reconsider using a creature of the same CR as the party's level. Otherwise, you might outright kill PCs before they get a chance to react. In our game last night, the level 5 party was surprised by a CR5 giant crocodile (a beast of size huge). The crocodile successfully bit the halfling rogue, and I rolled well. The bite did 27 hp of damage, leaving the rogue with 1hp. The crocodile came before the halfling in the initiative order. If I had rolled a 29 on a 3d10+5 damage roll when the crocodile's turn came up, the rogue would have been dead outright without getting a chance to act. If a creature at the same level as the party can do that, imagine what a creature of a higher CR could do.