1) Count the beats in quavers, so say you are looking at a bar of 7/8, count 7 with an accent on the first beat, even just playing the same note, just hit say an E hard, then softer 6 times, hit the E harder again (ooeerrr), this way you get used to what sort of timing you need for that time signature for now, and in future too.
2) Use something like guitar pro, and do leads over the top within guitar pro, while its not improvising, it gets you used to what note groupings fit within the time signature
Id say try to accent the notes which are strongest in the groove; i.e. if you're playing in 7/4 with a 4+3 feel, accent beats 1 and 5 or each bar. Or if its 11/8 with a 3+3+2+3 then accent beats 1, 4, 7 and 9. Once you've got that feel then try missing out certain accented notes and hitting the next one in time
You've really got to find the groove and lock it in your head. Just as you probably don't have to count along to a standard 4/4 backing, make yourself so comfortable with the way the riff flows that you don't need to be constantly counting along. Only once you're "feeling" it will you find that improvising coherent lines on top comes naturally. The more you do it, the more second nature it will become.
Sounds really simple but important. I don't really solo over odd counts but I do like playing them in riffs. Get the count down and a groove over the top and you're there. The groove may be irregular note groupings but you just have to get used to how the repetition works.
Pay attention to the beat, and don't syncopate too much until you know what you're doing. I'm an adamant supporter of grouping rhythmic divisions into twos and threes. Say that we have a measure of twelve. We could divide it into four 3's (compound, 3333), six 2's (simple, 222222), or two 3's and three 2's (odd, 33222/23232/32223/22323, etc.). Find where the meter is divided, and give it its proper emphasis. If you're playing over a divisive rhythm, finding the beat could be harder.